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