Roadmap

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

PyBEL

  • Performance improvements

    • Parallelization of parsing

    • On-the-fly validation with OLS or MIRIAM

Bio2BEL

  • 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

Data2BEL

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