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Drug repurposing through joint learning on knowledge graphs and literature

https://doi.org/10.1101/385617
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What this work says

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

inferredcites →https://doi.org/10.1007/978-3-642-38288-8_14openalex-snapshot
Bio2RDF Release 2: Improved Coverage, Interoperability and Provenance of Life Science Linked Data
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A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles
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Computational approaches in target identification and drug discovery
inferredcites →https://doi.org/10.1016/j.drudis.2012.05.016openalex-snapshot
Open PHACTS: semantic interoperability for drug discovery
inferredcites →https://doi.org/10.1016/j.jbi.2008.03.004openalex-snapshot
Bio2RDF: Towards a mashup to build bioinformatics knowledge systems
inferredcites →https://doi.org/10.1016/j.patrec.2005.10.010openalex-snapshot
An introduction to ROC analysis
inferredcites →https://doi.org/10.1016/j.websem.2008.05.001openalex-snapshot
OWL 2: The next step for OWL
inferredcites →https://doi.org/10.1038/75556openalex-snapshot
Gene Ontology: tool for the unification of biology
inferredcites →https://doi.org/10.1038/msb.2011.26openalex-snapshot
PREDICT: a method for inferring novel drug indications with application to personalized medicine
inferredcites →https://doi.org/10.1038/nature14539openalex-snapshot
Deep learning
inferredcites →https://doi.org/10.1038/nmeth.2810openalex-snapshot
Similarity network fusion for aggregating data types on a genomic scale
inferredcites →https://doi.org/10.1038/nrd3078openalex-snapshot
How to improve R&D productivity: the pharmaceutical industry's grand challenge
inferredcites →https://doi.org/10.1038/nrg3337openalex-snapshot
Text-mining solutions for biomedical research: enabling integrative biology
inferredcites →https://doi.org/10.1038/srep10888openalex-snapshot
Analysis of the human diseasome using phenotype similarity between common, genetic and infectious diseases
inferredcites →https://doi.org/10.1042/bj20150497openalex-snapshot
Repurposing metformin: an old drug with new tricks in its binding pockets
inferredcites →https://doi.org/10.1093/bib/bbn035openalex-snapshot
Literature mining in support of drug discovery
inferredcites →https://doi.org/10.1093/bib/bbr005openalex-snapshot
Literature mining, ontologies and information visualization for drug repurposing
inferredcites →https://doi.org/10.1093/bib/bbv066openalex-snapshot
Drug–target interaction prediction: databases, web servers and computational models
inferredcites →https://doi.org/10.1093/bioinformatics/btn162openalex-snapshot
Prediction of drug–target interaction networks from the integration of chemical and genomic spaces
inferredcites →https://doi.org/10.1093/bioinformatics/btt474openalex-snapshot
DNorm: disease name normalization with pairwise learning to rank
inferredcites →https://doi.org/10.1093/bioinformatics/btt765openalex-snapshot
The EBI RDF platform: linked open data for the life sciences
inferredcites →https://doi.org/10.1093/bioinformatics/btx275openalex-snapshot
Neuro-symbolic representation learning on biological knowledge graphs
inferredcites →https://doi.org/10.1093/bioinformatics/bty133openalex-snapshot
A novel computational approach for drug repurposing using systems biology
inferredcites →https://doi.org/10.1093/bioinformatics/bty259openalex-snapshot
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations
inferredcites →https://doi.org/10.1093/bioinformatics/bty559openalex-snapshot
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes
inferredcites →https://doi.org/10.1093/nar/gkh131openalex-snapshot
UniProt: the Universal Protein knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkq973openalex-snapshot
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
inferredcites →https://doi.org/10.1093/nar/gkr1011openalex-snapshot
STITCH 3: zooming in on protein-chemical interactions
inferredcites →https://doi.org/10.1093/nar/gkr972openalex-snapshot
Disease Ontology: a backbone for disease semantic integration
inferredcites →https://doi.org/10.1093/nar/gkt1026openalex-snapshot
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
inferredcites →https://doi.org/10.1093/nar/gkt441openalex-snapshot
PubTator: a web-based text mining tool for assisting biocuration
inferredcites →https://doi.org/10.1093/nar/gkv1075openalex-snapshot
The SIDER database of drugs and side effects
inferredcites →https://doi.org/10.1093/nar/gkw943openalex-snapshot
DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants
inferredcites →https://doi.org/10.1093/nar/gky092openalex-snapshot
UniProt: the universal protein knowledgebase
inferredcites →https://doi.org/10.1109/jbhi.2016.2636665openalex-snapshot
Deep Learning for Health Informatics
inferredcites →https://doi.org/10.1109/jproc.2015.2483592openalex-snapshot
A Review of Relational Machine Learning for Knowledge Graphs
inferredcites →https://doi.org/10.1142/9789812776136_0062openalex-snapshot
BANNER: AN EXECUTABLE SURVEY OF ADVANCES IN BIOMEDICAL NAMED ENTITY RECOGNITION
inferredcites →https://doi.org/10.1145/2623330.2623732openalex-snapshot
DeepWalk
inferredcites →https://doi.org/10.1155/2015/918710openalex-snapshot
GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains
inferredcites →https://doi.org/10.1186/1758-2946-7-s1-s3openalex-snapshot
tmChem: a high performance approach for chemical named entity recognition and normalization
inferredcites →https://doi.org/10.1186/s12859-016-1005-xopenalex-snapshot
Predicting drug target interactions using meta-path-based semantic network analysis
inferredcites →https://doi.org/10.1186/s13321-015-0089-zopenalex-snapshot
Optimizing drug–target interaction prediction based on random walk on heterogeneous networks
inferredcites →https://doi.org/10.1371/journal.pcbi.1000943openalex-snapshot
Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases
inferredcites →https://doi.org/10.1371/journal.pone.0035254openalex-snapshot
Predicting Anatomical Therapeutic Chemical (ATC) Classification of Drugs by Integrating Chemical-Chemical Interactions and Similarities
inferredcites →https://doi.org/10.15252/msb.20156651openalex-snapshot
Deep learning for computational biology
inferredcites →https://doi.org/10.1609/aaai.v30i1.10314openalex-snapshot
Holographic Embeddings of Knowledge Graphs
inferredcites →https://doi.org/10.2174/157340911795677602openalex-snapshot
Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
inferredcites →https://doi.org/10.3115/v1/d14-1162openalex-snapshot
Glove: Global Vectors for Word Representation
inferredcites →https://doi.org/10.3115/v1/d14-1167openalex-snapshot
Knowledge Graph and Text Jointly Embedding
inferredcites →https://doi.org/10.48550/arxiv.1201.0490openalex-snapshot
Scikit-learn: Machine Learning in Python

What points at this work

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

inferred← citeshttps://doi.org/10.1007/978-3-031-34960-7_24openalex-snapshot
Relation Predictions in Comorbid Disease Centric Knowledge Graph Using Heterogeneous GNN Models
inferred← citeshttps://doi.org/10.1007/s00044-025-03465-7openalex-snapshot
Comparative analysis on artificial intelligence methods for DTI and DTBA prediction in drug repurposing
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2025.108364openalex-snapshot
Knowledge graph applications and multi-relation learning for drug repurposing: A scoping review
inferred← citeshttps://doi.org/10.1016/j.jbi.2023.104528openalex-snapshot
EGeRepDR: An enhanced genetic-based representation learning for drug repurposing using multiple biomedical sources
inferred← citeshttps://doi.org/10.1016/j.sbi.2021.09.003openalex-snapshot
Toward better drug discovery with knowledge graph
inferred← citeshttps://doi.org/10.1016/j.sjbs.2021.03.068openalex-snapshot
A novel computational drug repurposing approach for Systemic Lupus Erythematosus (SLE) treatment using Semantic Web technologies
inferred← citeshttps://doi.org/10.1021/acsomega.3c00085openalex-snapshot
SS-GNN: A Simple-Structured Graph Neural Network for Affinity Prediction
inferred← citeshttps://doi.org/10.1038/s41597-024-04070-wopenalex-snapshot
Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data
inferred← citeshttps://doi.org/10.1038/s41598-022-08787-9openalex-snapshot
Affinity2Vec: drug-target binding affinity prediction through representation learning, graph mining, and machine learning
inferred← citeshttps://doi.org/10.1039/9781839163401-00147openalex-snapshot
Using Artificial Intelligence for Drug Repurposing
inferred← citeshttps://doi.org/10.1101/2023.02.11.528088openalex-snapshot
Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data
inferred← citeshttps://doi.org/10.1101/2025.08.11.666099openalex-snapshot
The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data
inferred← citeshttps://doi.org/10.1101/730085openalex-snapshot
Expanding a Database-derived Biomedical Knowledge Graph via Multi-relation Extraction from Biomedical Abstracts
inferred← citeshttps://doi.org/10.1109/nmitcon58196.2023.10275870openalex-snapshot
Drug Target Interaction Prediction by using Deep Learning Technique
inferred← citeshttps://doi.org/10.1109/tcbb.2019.2933825openalex-snapshot
An Analytical Review of Computational Drug Repurposing
inferred← citeshttps://doi.org/10.1186/s13040-022-00311-zopenalex-snapshot
Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts
inferred← citeshttps://doi.org/10.2174/1573409915666190613113822openalex-snapshot
Computational Drug Repurposing: Classification of the Research Opportunities and Challenges
inferred← citeshttps://doi.org/10.3389/fchem.2019.00782openalex-snapshot
Comparison Study of Computational Prediction Tools for Drug-Target Binding Affinities
inferred← citeshttps://doi.org/10.6084/m9.figshare.21358086openalex-snapshot
Additional file 1 of Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts
inferred← citeshttps://doi.org/10.7717/peerj-cs.341openalex-snapshot
Application and evaluation of knowledge graph embeddings in biomedical data
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