ArticleGenome biology2020
Pathway information extracted from 25 years of pathway figures.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed.
- The graphical abstract.Nature methods · 2026Article
- Protein Predictors of Worsening Cerebral Edema in Traumatic Brain Injury in Critically Ill Patients.bioRxiv : the preprint server for biology · 2026Article
- Article
- GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.GigaScience · 2025Article
- In silico and functional analysis identifies key gene networks and novel gene candidates in obesity-linked human visceral fat.Obesity (Silver Spring, Md.) · 2024Article
- Prediction of immunotherapy response using mutations to cancer protein assemblies.Science advances · 2024Article
- pathCLIP: Detection of Genes and Gene Relations From Biological Pathway Figures Through Image-Text Contrastive Learning.IEEE journal of biomedical and health informatics · 2024Article
- WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics.Nucleic acids research · 2024Article
- Rummagene: massive mining of gene sets from supporting materials of biomedical research publications.Communications biology · 2024Article
- WikiPathways 2024: next generation pathway database.Nucleic acids research · 2024Article
- Using published pathway figures in enrichment analysis and machine learning.BMC genomics · 2023Article
- pathCLIP: Detection of Genes and Gene Relations from Biological Pathway Figures through Image-Text Contrastive Learning.bioRxiv : the preprint server for biology · 2023Article
- Enrichr-KG: bridging enrichment analysis across multiple libraries.Nucleic acids research · 2023Article
- Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing.ArXiv · 2023Article
- Applications of cutting-edge artificial intelligence technologies in biomedical literature and document mining.Medical review (2021) · 2023Article
- Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations.Orphanet journal of rare diseases · 2023Article
- NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.Bioinformatics (Oxford, England) · 2023Article
- Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.Briefings in bioinformatics · 2022Article
- On the influence of several factors on pathway enrichment analysis.Briefings in bioinformatics · 2022Review
- Molecular cartooning with knowledge graphs.Frontiers in bioinformatics · 2022Article
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
Thousands of pathway diagrams are published each year as static figures inaccessible to computational queries and analyses. Using a combination of machine learning, optical character recognition, and manual curation, we identified 64,643 pathway figures published between 1995 and 2019 and extracted 1,112,551 instances of human genes, comprising 13,464 unique NCBI genes, participating in a wide variety of biological processes. This collection represents an order of magnitude more genes than found in the text of the same papers, and thousands of genes missing from other pathway databases, thus presenting new opportunities for discovery and 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.