ArticleDatabase : the journal of biological databases and curation2018
Large-scale automated machine reading discovers new cancer-driving mechanisms.
Article in Database : the journal of biological databases and curation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- From prior knowledge to data-informed models: a review of Boolean network inference.Briefings in bioinformatics · 2026Review
- VIOLIN: A modular framework for scalable reconciliation of heterogeneous interaction graphs.bioRxiv : the preprint server for biology · 2026Article
- A Computational Protocol for the Knowledge-Based Assessment and Capture of Pathologies.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Computational tools and data integration to accelerate vaccine development: challenges, opportunities, and future directions.Frontiers in immunology · 2025Review
- Beyond protein lists: AI-assisted interpretation of proteomic investigations in the context of evolving scientific knowledge.Nature methods · 2024Article
- Semantics-enabled biomedical literature analytics.Journal of biomedical informatics · 2024Article
- Context-aware knowledge selection and reliable model recommendation with ACCORDION.Frontiers in systems biology · 2024Article
- Automated assembly of molecular mechanisms at scale from text mining and curated databases.Molecular systems biology · 2023Article
- Developing a Knowledge Graph for Pharmacokinetic Natural Product-Drug Interactions.Journal of biomedical informatics · 2023Article
- NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.Bioinformatics (Oxford, England) · 2023Article
- RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine.BMC bioinformatics · 2022Article
- Automated Network Assembly of Mechanistic Literature for Informed Evidence Identification to Support Cancer Risk Assessment.Environmental health perspectives · 2022Article
- Gilda: biomedical entity text normalization with machine-learned disambiguation as a service.Bioinformatics advances · 2022Article
- YTLR: Extracting yeast transcription factor-gene associations from the literature using automated literature readers.Computational and structural biotechnology journal · 2022Article
- Article
- Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms' representation.BioData mining · 2021Article
- The role of metadata in reproducible computational research.Patterns (New York, N.Y.) · 2021Review
- Causal interactions from proteomic profiles: Molecular data meet pathway knowledge.Patterns (New York, N.Y.) · 2021Article
- Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis.IEEE transactions on big data · 2021Article
- GeneWalk identifies relevant gene functions for a biological context using network representation learning.Genome biology · 2021Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
PubMed, a repository and search engine for biomedical literature, now indexes >1 million articles each year. This exceeds the processing capacity of human domain experts, limiting our ability to truly understand many diseases. We present Reach, a system for automated, large-scale machine reading of biomedical papers that can extract mechanistic descriptions of biological processes with relatively high precision at high throughput. We demonstrate that combining the extracted pathway fragments with existing biological data analysis algorithms that rely on curated models helps identify and explain a large number of previously unidentified mutually exclusive altered signaling pathways in seven different cancer types. This work shows that combining human-curated 'big mechanisms' with extracted 'big data' can lead to a causal, predictive understanding of cellular processes and unlock important downstream applications.
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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.