Semantic Web in Systems Chemical Biology

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Recent advances in high throughput techniques have generated biological data in myriad volumes, which simultaneously contributes to a newly emerged discipline -- system biology, which adopts a comprehensive approach to study biological systems. Chemogenomics, as an integrated part of system biology, studies the impact of small molecules towards biological systems and carries datum description about interaction among chemical entities and protein molecules. The integration between chemical informatics and bioinformatics within the realm of system biology leads to a new synergetic subject, namely systems chemical biology(ref).

However, the current de facto of chemical and biological data distribution impedes the growth of systems chemical biology due to heterogeneous formats used. This project is dedicated to address such challenges using existing semantic web technology, in particular bio2rdf, Linking open drug data. Beyond the generic scopes of these two initiatives, we are also planning to incorporate new semantic clauses to embed the core interests of system chemical biology, for instance chemical structural similarity and biological sequence similarity. Figure 1 shows the overall scope of systems chemical biology.

Figure 1: Linking data in systems chemical biology. Chemical includes small compounds being tested as well as drugs.Biology includes protein and gene, Systems includes protein protein interaction, metabolic pathways, regulatory network and so on. Phenotype includes disease, side effects and toxicity.

Table of Contents:

  1. Datasets
  2. Ontology
  3. Use cases:
    1. Case 1: Adverse Drug Reaction
    2. Case 2: Polypharmacology
    3. Case 3: Disease specific chemicals discovery and ranking
    4. PXR study
  4. References
  5. Demos and applications
    1. Browse RDF
    2. Demo of Chem2Bio2RDF
    3. Cytoscape Plugin
    4. Applications
    5. Search in
    6. Extraction of Biological, Chemical Networks from Bio2RDF, LODD and Chem2Bio2RDF
    7. Ontology Driven Data Exploration of Chem2Bio2RDF
  6. Developer notes
    1. Chem2Bio2RDF architecture
    2. Q & A
    3. Development Environment setup
    4. How to add a new dataset into Chem2Bio2RDF
    5. Namespace
    6. Naming convention
    7. SPARQL Endpoints
    8. Link2Sparql Concretizer
    9. Integrate with ChEMBL
    10. How to publish data using D2R?
    11. Workflow for update to ChEMBL_15 (IN PROGRESS).
  7. Misc
    1. Status of project
    2. PlotViz for SPARQL results
    3. Automated Linked Path Generation
    4. Key properties


Bin Chen (
Jeremy Yang (
Xiao Dong
Dazhi Jiao
Huijun Wang
Qian Zhu
David Wild (advisor)
Ying Ding (advisor)