ArticlePLoS computational biology2013
Getting more out of biomedical documents with GATE's full lifecycle open source text analytics.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 papers, 4 of them syntheses that pooled it.
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
103 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Natural Language Processing Applications in the Clinical Neurosciences: A Machine Learning Augmented Systematic Review.Acta neurochirurgica. Supplement · 2022Pooled it
- The Potential of Research Drawing on Clinical Free Text to Bring Benefits to Patients in the United Kingdom: A Systematic Review of the Literature.Frontiers in digital health · 2021Pooled it
- Natural language processing systems for capturing and standardizing unstructured clinical information: A systematic review.Journal of biomedical informatics · 2017Pooled it
- Text mining applications in psychiatry: a systematic literature review.International journal of methods in psychiatric research · 2016Pooled it
- Natural Language Processing Applied to Psychiatric Clinical Notes: Scoping Review.JMIR medical informatics · 2026Article
- Article
- Late-life affective disorders and risk of progression to dementia: retrospective cohort study of patients in secondary care.The British journal of psychiatry : the journal of mental science · 2026Article
- VIEWER: an extensible visual analytics framework for enhancing mental healthcare.Journal of the American Medical Informatics Association : JAMIA · 2026Article
- Developing clinical informatics to support direct care and population health management: the VIEWER story.BMJ health & care informatics · 2025Article
- Cognitive trajectories and dementia risk in patients with schizophrenia spectrum versus affective disorders.Psychological medicine · 2025Article
- Mood instability as a transdiagnostic predictor of cannabis use in attention-deficit/hyperactivity disorder and depression: A natural language processing analysis of electronic health records from 13,025 adolescents.European psychiatry : the journal of the Association of European Psychiatrists · 2025Article
- Identifying people with potentially undiagnosed dementia with Lewy bodies using natural language processing.npj aging · 2025Article
- Diagnosis extraction from unstructured Dutch echocardiogram reports using span- and document-level characteristic classification.BMC medical informatics and decision making · 2025Article
- PretoxTM: a text mining system for extracting treatment-related findings from preclinical toxicology reports.Journal of cheminformatics · 2025Article
- Who you gonna call? Examining police reports involving people with psychosis to improve front line management.Frontiers in psychiatry · 2025Article
- Population Characteristics in Justice Health Research Based on PubMed Abstracts From 1963 to 2023: Text Mining Study.JMIR formative research · 2024Article
- Obsessive-compulsive symptoms relating to psychosocial functioning for people with schizophrenia, schizoaffective disorder, or bipolar disorder.Acta neuropsychiatrica · 2024Article
- Understanding social and clinical associations with unemployment for people with schizophrenia and bipolar disorders: large-scale health records study.Social psychiatry and psychiatric epidemiology · 2024Article
- Generating Complex Explanations for Artificial Intelligence Models: An Application to Clinical Data on Severe Mental Illness.Life (Basel, Switzerland) · 2024Article
- An analysis of published study designs in PubMed prisoner health abstracts from 1963 to 2023: a text mining study.BMC medical research methodology · 2024Review
43 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
This software article describes the GATE family of open source text analysis tools and processes. GATE is one of the most widely used systems of its type with yearly download rates of tens of thousands and many active users in both academic and industrial contexts. In this paper we report three examples of GATE-based systems operating in the life sciences and in medicine. First, in genome-wide association studies which have contributed to discovery of a head and neck cancer mutation association. Second, medical records analysis which has significantly increased the statistical power of treatment/outcome models in the UK's largest psychiatric patient cohort. Third, richer constructs in drug-related searching. We also explore the ways in which the GATE family supports the various stages of the lifecycle present in our examples. We conclude that the deployment of text mining for document abstraction or rich search and navigation is best thought of as a process, and that with the right computational tools and data collection strategies this process can be made defined and repeatable. The GATE research programme is now 20 years old and has grown from its roots as a specialist development tool for text processing to become a rather comprehensive ecosystem, bringing together software developers, language engineers and research staff from diverse fields. GATE now has a strong claim to cover a uniquely wide range of the lifecycle of text analysis systems. It forms a focal point for the integration and reuse of advances that have been made by many people (the majority outside of the authors' own group) who work in text processing for biomedicine and other areas. GATE is available online <1> under GNU open source licences and runs on all major operating systems. Support is available from an active user and developer community and also on a commercial basis.
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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.