Collapse All Variants
Collapse all genes', RNAs', miRNAs', and proteins' variants to their parents.
Collapse Consistent Edges
Collapse consistent edges together.
Collapse Entrez Equivalencies
Collapse all equivalence edges away from Entrez. Assumes well formed, 2-way equivalencies.
Collapse Entrez To Hgnc
Collapse Entrez equivalences to HGNC.
Collapse Flybase To Hgnc
Collapse FlyBase orthologies to HGNC.
Collapse Gene Variants
Collapse all gene's variants' edges to their parents, in-place.
Collapse Mgi To Hgnc
Collapse MGI orthologies to HGNC.
Collapse Protein Variants
Collapse all protein's variants' edges to their parents, in-place.
Collapse Rgd To Hgnc
Collapse RGD orthologies to HGNC.
Collapse To Genes
Collapse all protein, RNA, and miRNA nodes to their corresponding gene nodes.
Collapse To Protein Interactions
Collapse to a graph made of only causal gene/protein edges.
Enrich Complexes
Add all of the members of the complex abundances to the graph.
Enrich Composites
Adds all of the members of the composite abundances to the graph.
Enrich Internal Unqualified Edges
Add the missing unqualified edges between entities in the subgraph that are contained within the full graph.
Enrich Protein And Rna Origins
Add the corresponding RNA for each protein then the corresponding gene for each RNA/miRNA.
Enrich Proteins With Rnas
Add the corresponding RNA node for each protein node and connect them with a translation edge.
Enrich Reactions
Adds all of the reactants and products of reactions to the graph.
Enrich Rnas With Genes
Add the corresponding gene node for each RNA/miRNA node and connect them with a transcription edge.
Enrich Unqualified
Enrich the sub-graph with the unqualified edges from the graph.
Enrich Variants
Add the reference nodes for all variants of the given function.
Expand Downstream Causal
Add the downstream causal relations to the given sub-graph.
Expand Internal Causal
Add causal edges between entities in the sub-graph.
Expand Upstream Causal
Add the upstream causal relations to the given sub-graph.
Get Causal Subgraph
Build a new sub-graph induced over the causal edges.
Get Largest Component
Get the giant component of a graph.
Highlight Subgraph
Highlight all nodes/edges in the universe that in the given graph.
Infer Missing Two Way Edges
Add edges to the graph when a two way edge exists, and the opposite direction doesn't exist.
Prune Protein Origins
Delete RNA nodes that are only connected to one node - their correspond protein - by a translation edge.
Prune Protein Rna Origins
Delete genes that are only connected to one node, their correspond RNA, by a translation edge.
Prune Rna Origins
Delete gene nodes that are only connected to one node, their correspond RNA, by a transcription edge.
Remove Associations
Remove all associative relationships from the graph.
Remove Biological Processes
Remove biological process nodes from the graph.
Remove Citation Metadata
Remove the metadata associated with a citation.
Remove Inconsistent Edges
Remove all edges between node pairs with inconsistent edges.
Remove Isolated List Abundances
Remove isolated list abundances from the graph.
Remove Isolated Nodes
Remove isolated nodes from the network, in place.
Remove Isolated Nodes Op
Build a new graph excluding the isolated nodes.
Remove Mouse Nodes
Remove nodes using the MGI and MGIID namespaces.
Remove Pathologies
Remove pathology nodes from the graph.
Remove Rat Nodes
Remove nodes using the RGD and RGDID namespaces.
Rewire Variants To Genes
Find all protein variants that are pointing to a gene and not a protein and fixes them by changing their
function to be :data:`pybel.constants.GENE`, in place
Strip Annotations
Strip all the annotations from a BEL graph.
Update Context
Updates the context of a subgraph from the universe of all knowledge.
