ArticleNucleic acids research2019
PubTator central: automated concept annotation for biomedical full text articles.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 208 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
208 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- The characteristics of early-stage research into human genes are substantially different from subsequent research.PLoS biology · 2022Pooled it
- Exploration of the core protein network under endometriosis symptomatology using a computational approach.Frontiers in endocrinology · 2022Pooled it
- SARS-CoV-2 Causes a Different Cytokine Response Compared to Other Cytokine Storm-Causing Respiratory Viruses in Severely Ill Patients.Frontiers in immunology · 2021Pooled it
- ACE2 Expression Is Increased in the Lungs of Patients With Comorbidities Associated With Severe COVID-19.The Journal of infectious diseases · 2020Pooled it
- Literature-informed gene extraction and ranking for multimodal data fusion.Briefings in bioinformatics · 2026Article
- From narrative evidence to computable knowledge: a decision-relevant corpus for medicinal herb-disease relationships.Journal of biomedical semantics · 2026Article
- Mining Two Decades of Soybean Genomics Literature Using Rule-Based Text Mining: Chromosome-Resolved Patterns ofInternational journal of molecular sciences · 2026Article
- Ontology-driven association rule mining for biomedical entity relationships: integrating hierarchical knowledge to improve gene-disease discovery.Scientific reports · 2026Article
- datadrivenhypothesis.org: A resource for metabolic gene discovery through integrated pathway co-essentiality mapping.bioRxiv : the preprint server for biology · 2026Article
- A practical and nuanced framework for entity linking evaluation.Journal of biomedical semantics · 2026Article
- Integrating curation into scientific publishing to train AI models.Bioinformatics (Oxford, England) · 2026Article
- DriverSub-SVM: a machine learning approach for cancer subtype classification by integrating patient-specific and global driver genes.BMC bioinformatics · 2025Article
- Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.G3 (Bethesda, Md.) · 2025Article
- Knowledge-augmented pre-trained language models for biomedical relation extraction.BMC bioinformatics · 2025Article
- Unlocking biological insights from differentially expressed genes: Concepts, methods, and future perspectives.Journal of advanced research · 2025Review
- Evaluating Language Models for Biomedical Fact-Checking: A Benchmark Dataset for Cancer Variant Interpretation Verification.bioRxiv : the preprint server for biology · 2025Article
- Regulation of Tetraspanin CD63 in Chronic Myeloid Leukemia (CML): Single-Cell Analysis of Asymmetric Hematopoietic Stem Cell Division Genes.Bioengineering (Basel, Switzerland) · 2025Article
- A conceptual framework for human-AI collaborative genome annotation.Briefings in bioinformatics · 2025Review
- CSpace: a concept embedding space for biomedical applications.Bioinformatics (Oxford, England) · 2025Article
- Text Mining Strategy Identifies Gene Networks Under Control of miR-21 in Breast Cancer Development.Cancer medicine · 2025Article
148 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
PubTator Central (https://www.ncbi.nlm.nih.gov/research/pubtator/) is a web service for viewing and retrieving bioconcept annotations in full text biomedical articles. PubTator Central (PTC) provides automated annotations from state-of-the-art text mining systems for genes/proteins, genetic variants, diseases, chemicals, species and cell lines, all available for immediate download. PTC annotates PubMed (29 million abstracts) and the PMC Text Mining subset (3 million full text articles). The new PTC web interface allows users to build full text document collections and visualize concept annotations in each document. Annotations are downloadable in multiple formats (XML, JSON and tab delimited) via the online interface, a RESTful web service and bulk FTP. Improved concept identification systems and a new disambiguation module based on deep learning increase annotation accuracy, and the new server-side architecture is significantly faster. PTC is synchronized with PubMed and PubMed Central, with new articles added daily. The original PubTator service has served annotated abstracts for ∼300 million requests, enabling third-party research in use cases such as biocuration support, gene prioritization, genetic disease analysis, and literature-based knowledge discovery. We demonstrate the full text results in PTC significantly increase biomedical concept coverage and anticipate this expansion will both enhance existing downstream applications and enable new use cases.
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.