ArticleBioinformatics (Oxford, England)2023
KG-Hub-building and exchanging biological knowledge graphs.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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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
21 citing papers in PubMed.
- Graph-based representations in modern protein science.The Biochemical journal · 2026Review
- RNA-KG v2.0: an RNA-centered Knowledge Graph with Properties.NAR genomics and bioinformatics · 2026Article
- SPHN Connector - a scalable pipeline for generating validated knowledge graphs from federated and semantically enriched health data.BMC medical informatics and decision making · 2026Article
- KG-Microbe: Building modular and scalable knowledge graphs for microbiome and microbial sciences.GigaScience · 2026Article
- Turning data into insights in Jub, an extensible generic big data platform for life science and healthcare applications.Scientific reports · 2025Article
- Graph Neural Network-Based Toxicity Prediction by Integrating Molecular Fingerprints and Knowledge Graph Features.Toxics · 2025Article
- monarchr: an R package for querying biomedical knowledge graphs.Bioinformatics (Oxford, England) · 2025Article
- Creating an Interactive Web Interface for Networks Stored in Knowledge Graph Databases.Current protocols · 2025Article
- Microbiome knowledge graph as a tool to understand bacteria-host associations.Archives of microbiology · 2025Article
- BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies.Nucleic acids research · 2025Article
- Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs.BMC medical informatics and decision making · 2025Article
- OLS4: a new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem.Bioinformatics (Oxford, England) · 2025Article
- A change language for ontologies and knowledge graphs.Database : the journal of biological databases and curation · 2025Article
- Knowledge Representation and Management: 2023 Highlights and the Rise of Knowledge Graph Embeddings.Yearbook of medical informatics · 2024Review
- Article
- NetMe 2.0: a web-based platform for extracting and modeling knowledge from biomedical literature as a labeled graph.Bioinformatics (Oxford, England) · 2024Article
- An open source knowledge graph ecosystem for the life sciences.Scientific data · 2024Article
- The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.Nucleic acids research · 2024Article
- Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning.Bioinformatics advances · 2024Article
- Using knowledge graphs to infer gene expression in plants.Frontiers in artificial intelligence · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
26 authors.
Funding
Abstract
motivationKnowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of KGs is lacking.
resultsHere we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of KGs. Features include a simple, modular extract-transform-load pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial-environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate KGs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph ML, including node embeddings and training of models for link prediction and node classification. AVAILABILITY AND IMPLEMENTATION: https://kghub.org.
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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.