pkoi_net: Human-Specific Protein Knowledge Graph
pkoi_net.Rd`pkoi_net` is a precomputed, undirected, heterogeneous knowledge graph that integrates proteomic, genomic, and functional annotations for network-aware omics analyses using the `pkoi` package.
Usage
data(pkoi_net)Format
An `igraph` object with:
- 939,059 vertices
Each vertex represents a biological entity and includes the following attributes:
name,labels,identifier, and precomputed network statistics:degree,coreness,betweenness,closeness,constraint,eccentricity,eigen_centrality,transitivity.- 10,622,200 edges
Each edge encodes a biological relationship with attribute:
edge_type– a character string describing the relationship type.
Node types included in the graph:
- Anatomy
Anatomical structures and systems
- BiologicalProcess
Functional biological processes such as signaling pathways
- CellType
Distinct cell types
- CellularComponent
Subcellular structures and organelles
- ClinicalLab
Clinical measurements and diagnostics
- Complex
Molecular and protein complexes
- Compound
Endogenous human metabolites
- Disease
Diseases and pathological conditions
- EC
Enzyme Commission categories
- Gene
Genetic elements including genes and markers
- MiRNA
MicroRNAs and their regulatory roles
- MolecularFunction
Molecular-level activities of gene products
- Pathway
Molecular interaction and reaction sequences
- Protein
Protein molecules
- ProteinDomain
Structural or functional domains within proteins
- ProteinFamily
Groups of evolutionarily related proteins
- PwGroup
Aggregates of related pathways
- Reaction
Biochemical reactions