Transformations

Collapse All Variants

Collapse all genes', RNAs', miRNAs', and proteins' variants to their parents.

Collapse Consistent Edges

Collapse consistent edges together.

Collapse Entrez Equivalencies

Collapses 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

Collapses all gene's variants' edges to their parents, in-place

Collapse Mgi To Hgnc

Collapse MGI orthologies to HGNC.

Collapse Protein Variants

Collapses 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

Adds 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 subgraph with the unqualified edges from the graph.

Expand Downstream Causal

Add the downstream causal relations to the given sub-graph.

Expand Internal Causal

Adds causal edges between entities in the subgraph.

Expand Upstream Causal

Add the upstream causal relations to the given sub-graph.

Get Causal Subgraph

Builds a new subgraph induced over all edges that are causal

Get Largest Component

Gets the giant component of a subgraph

Highlight Subgraph

Highlights all nodes/edges in the universe that in the given graph.

Infer Missing Two Way Edges

If a two way edge exists, and the opposite direction doesn't exist, add it to the graph

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 Inconsistent Edges

Remove all edges between node paris with consistent edges.

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

Finds 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.

About

BEL Commons is developed and maintained in an academic capacity by Charles Tapley Hoyt and Daniel Domingo-Fernández at the Fraunhofer SCAI Department of Bioinformatics with support from the IMI project, AETIONOMY. It is built on top of the open source project, PyBEL. Please feel free to contact us here to give us feedback or report any issues.