ReviewBriefings in bioinformatics2016
Community challenges in biomedical text mining over 10 years: success, failure and the future.
Review in Briefings in bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers, 1 of them a synthesis 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
88 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The role of machine learning in developing non-magnetic resonance imaging based biomarkers for multiple sclerosis: a systematic review.BMC medical informatics and decision making · 2022Pooled it
- Methodological information extraction from randomized controlled trial publications: a pilot study.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2022Trial
- A text mining and ontology-based approach using phenotypes to obtain relevant literature for rare diseases.iScience · 2026Article
- Article
- RECODE - Relational Ecological COrpus for Data Extraction.Biodiversity data journal · 2026Article
- 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
- Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes.Database : the journal of biological databases and curation · 2024Article
- Identifying symptom etiologies using syntactic patterns and large language models.Scientific reports · 2024Article
- DUVEL: an active-learning annotated biomedical corpus for the recognition of oligogenic combinations.Database : the journal of biological databases and curation · 2024Article
- MetaTron: advancing biomedical annotation empowering relation annotation and collaboration.BMC bioinformatics · 2024Article
- Secondary Use of Clinical Problem List Descriptions for Bi-Encoder Based ICD-10 Classification.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2024Article
- Dictionary-based matching graph network for biomedical named entity recognition.Scientific reports · 2023Article
- Combining unsupervised, supervised and rule-based learning: the case of detecting patient allergies in electronic health records.BMC medical informatics and decision making · 2023Article
- GePI: large-scale text mining, customized retrieval and flexible filtering of gene/protein interactions.Nucleic acids research · 2023Article
- Linguistic and ontological challenges of multiple domains contributing to transformed health ecosystems.Frontiers in medicine · 2023Article
- Elaboration of a new framework for fine-grained epidemiological annotation.Scientific data · 2022Article
- Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.Database : the journal of biological databases and curation · 2022Article
- Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification.Database : the journal of biological databases and curation · 2022Article
- A biomedical event extraction method based on fine-grained and attention mechanism.BMC bioinformatics · 2022Article
28 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
2 authors.
Funding
Abstract
One effective way to improve the state of the art is through competitions. Following the success of the Critical Assessment of protein Structure Prediction (CASP) in bioinformatics research, a number of challenge evaluations have been organized by the text-mining research community to assess and advance natural language processing (NLP) research for biomedicine. In this article, we review the different community challenge evaluations held from 2002 to 2014 and their respective tasks. Furthermore, we examine these challenge tasks through their targeted problems in NLP research and biomedical applications, respectively. Next, we describe the general workflow of organizing a Biomedical NLP (BioNLP) challenge and involved stakeholders (task organizers, task data producers, task participants and end users). Finally, we summarize the impact and contributions by taking into account different BioNLP challenges as a whole, followed by a discussion of their limitations and difficulties. We conclude with future trends in BioNLP challenge evaluations.
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.