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Automated assembly of molecular mechanisms at scale from text mining and curated databases

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Defining a Cancer Dependency Map
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Gene Ontology: tool for the unification of biology
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Differential control of TAp73 and ΔNp73 protein stability by the ring finger ubiquitin ligase PIR2
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Grb10 Inhibits Insulin-stimulated Insulin Receptor Substrate (IRS)-Phosphatidylinositol 3-Kinase/Akt Signaling Pathway by Disrupting the Association of IRS-1/IRS-2 with the Insulin Receptor
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Growth Factor Receptor-binding Protein 10 (Grb10) as a Partner of Phosphatidylinositol 3-Kinase in Metabolic Insulin Action
inferredcites →https://doi.org/10.1074/jbc.m305622200openalex-snapshot
Myosin Phosphatase-Rho Interacting Protein
inferredcites →https://doi.org/10.1086/670067openalex-snapshot
emcee : The MCMC Hammer
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Gilda: biomedical entity text normalization with machine-learned disambiguation as a service
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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
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MedScan, a natural language processing engine for MEDLINE abstracts
inferredcites →https://doi.org/10.1093/bioinformatics/btp665openalex-snapshot
ChiBE: interactive visualization and manipulation of BioPAX pathway models
inferredcites →https://doi.org/10.1093/bioinformatics/btq221openalex-snapshot
PathText: a text mining integrator for biological pathway visualizations
inferredcites →https://doi.org/10.1093/database/baaa056openalex-snapshot
FLUTE: Fast and reliable knowledge retrieval from biomedical literature
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Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine
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The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets
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Human protein reference database--2006 update
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PID: The Pathway Interaction Database
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STRING 8--a global view on proteins and their functional interactions in 630 organisms
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Pathway Commons, a web resource for biological pathway data
inferredcites →https://doi.org/10.1093/nar/gkr1122openalex-snapshot
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
inferredcites →https://doi.org/10.1093/nar/gkv1031openalex-snapshot
ChEBI in 2016: Improved services and an expanding collection of metabolites
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SIGNOR: a database of causal relationships between biological entities
inferredcites →https://doi.org/10.1093/nar/gkv1351openalex-snapshot
The Reactome pathway Knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkx1132openalex-snapshot
The Reactome Pathway Knowledgebase
inferredcites →https://doi.org/10.1093/nar/gky1049openalex-snapshot
UniProt: a worldwide hub of protein knowledge
inferredcites →https://doi.org/10.1093/nar/gky1079openalex-snapshot
The BioGRID interaction database: 2019 update
inferredcites →https://doi.org/10.1093/nar/gkz946openalex-snapshot
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data
inferredcites →https://doi.org/10.1101/2020.04.02.022277openalex-snapshot
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inferredcites →https://doi.org/10.1109/tcbb.2014.2372765openalex-snapshot
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inferredcites →https://doi.org/10.1109/tcbb.2019.2904231openalex-snapshot
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inferredcites →https://doi.org/10.1145/3308558.3313586openalex-snapshot
Triple Trustworthiness Measurement for Knowledge Graph
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inferredcites →https://doi.org/10.1161/circresaha.108.188524openalex-snapshot
ROCK Isoform Regulation of Myosin Phosphatase and Contractility in Vascular Smooth Muscle Cells
inferredcites →https://doi.org/10.1177/001316447903900302openalex-snapshot
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Automated assembly of molecular mechanisms at scale from text mining and curated databases
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Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Demonstrations
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Eidos, INDRA, & Delphi: From Free Text to Executable Causal Models
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Complex Event Extraction using DRUM
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Proceedings of the BioNLP 2018 workshop
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Understanding the Polarity of Events in the Biomedical Literature: Deep Learning vs. Linguistically-informed Methods
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Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature
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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Agentic AI for Computational Pharmacology: Orchestrating Molecular Search, Evidence Appraisal, Mechanistic Reasoning, and Candidate Prioritization
inferred← citeshttps://doi.org/10.7717/peerj.15815openalex-snapshot
Predicting protein and pathway associations for understudied dark kinases using pattern-constrained knowledge graph embedding
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