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Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
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cMapper: gene-centric connectivity mapper for EBI-RDF platform.

Muhammad Shoaib1,2, Adnan Ahmad Ansari1,2, Sung-Min Ahn2,3,4

  • 1Department of Biomedical Engineering, College of Medicine, University of Ulsan, Asan Medical Center, Seoul, Republic of Korea.

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Summary

cMapper simplifies biological data exploration by enabling gene-centric searches across integrated databases without requiring expertise in RDF or SPARQL.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Biological big data necessitates efficient data integration strategies.
  • Resource Description Framework (RDF) facilitates interoperability of heterogeneous biological datasets.
  • Existing platforms like EBI-RDF require specialized knowledge of RDF and SPARQL.

Purpose of the Study:

  • To develop a user-friendly tool for biologists to search integrated biological databases.
  • To overcome the technical barrier of RDF and SPARQL for accessing EBI-RDF data.
  • To enable gene-centric data exploration in multiple biological contexts.

Main Methods:

  • Developed cMapper, a web-based tool for gene-centric database searching.
  • Integrated six independent biological databases using RDF technologies and shared ontologies.
  • Implemented a user interface with Java, HTML5, JQuery, and Cytoscape Graph API.

Main Results:

  • cMapper allows searching connected data entities for genes or small molecules.
  • Outputs are visualized as interactive graphs with filtering options by database, taxonomy, organ, and pathways.
  • Users can investigate shared connections and download results in GraphML or JSON formats.

Conclusions:

  • cMapper provides an accessible interface for biologists to leverage integrated biological data.
  • The tool enhances biological data exploration without deep technical expertise.
  • cMapper facilitates discovery of relationships between genes, small molecules, and biological entities.