Chem2Bio2RDF: A Linked Open Data Portal for Chemical Biology
Bin Chen (1), David J Wild (1), Qian Zhu (1), Ying Ding (2), Xiao Dong, (1), Madhuvanthi Sankaranarayanan (1), Huijun Wang (1), Yuyin Sun (2) ((1), School of Informatics, Computing, Indiana University, Bloomington, IN,, USA, (2) School of Library, Information Science
TL;DR
Chem2Bio2RDF is a comprehensive linked data portal integrating diverse chemical biology datasets into RDF format, enabling advanced querying, visualization, and validation tools to facilitate drug discovery research.
Contribution
It introduces a unified portal that converts multiple datasets into RDF, linking them with other LOD sources and providing unique tools for querying and visualization.
Findings
Successfully integrated 25 datasets into RDF format.
Provides a user-friendly SPARQL query generator.
Demonstrates utility through three practical use cases.
Abstract
The Chem2Bio2RDF portal is a Linked Open Data (LOD) portal for systems chemical biology aiming for facilitating drug discovery. It converts around 25 different datasets on genes, compounds, drugs, pathways, side effects, diseases, and MEDLINE/PubMed documents into RDF triples and links them to other LOD bubbles, such as Bio2RDF, LODD and DBPedia. The portal is based on D2R server and provides a SPARQL endpoint, but adds on few unique features like RDF faceted browser, user-friendly SPARQL query generator, MEDLINE/PubMed cross validation service, and Cytoscape visualization plugin. Three use cases demonstrate the functionality and usability of this portal.
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Taxonomy
TopicsBiomedical Text Mining and Ontologies · Microbial Natural Products and Biosynthesis · Pharmacogenetics and Drug Metabolism