This project road map documents not only the PyBEL repository, but the PyBEL Tools and BEL Commons repositories as well as the Bio2BEL project.


  • Performance improvements
    • Parallelization of parsing
    • On-the-fly validation with OLS or MIRIAM


  • Generation of new namespaces, equivalencies, and hierarchical knowledge (isA and partOf relations)
    • FlyBase
    • InterPro (Done)
    • UniProt (Done)
    • Human Phenotype Ontology
    • Uber Anatomy Ontology
    • HGNC Gene Families (Done)
    • Enyzme Classification (Done)
  • Integration of knowledge sources
    • ChEMBL
    • Comparative Toxicogenomics Database (Done)
    • BRENDA
    • MetaCyc
    • Protein complex definitions


Integration of analytical pipelines to convert data to BEL

  • LD Block Analysis
  • Gene Co-expression Analysis
  • Differential Gene Expression Analysis

PyBEL Tools

  • Biological Grammar
    • Network motif identification
    • Stability analysis
    • Prior knowledge comparision
      • Molecular activity annotation
      • SNP Impact
  • Implementation of standard BEL Algorithms
    • RCR
    • NPA
    • SST
  • Development of new algorithms
    • Heat diffusion algorithms
    • Cart Before the Horse
  • Metapath analysis
  • Reasoning and inference rules
  • Subgraph Expansion application in NeuroMMSigDB
  • Chemical Enrichment in NeuroMMSigDB

BEL Commons

  • Integration with BELIEF
  • Integration with NeuroMMSigDB (Done)
  • Import and export from NDEx