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Data Representation


The pathway-level integration is not a simple collection of pathways and gene lists, but each signaling step was remodeled to represent pathways from different sources in a coherent fashion. Entities in the reformatted pathways were integrated at the molecular level to create a unified super-pathway.


Pathway-level data modeling

Entity

Entities are classified into proteins, genes, compounds or complexes. A compound is any entity that is not a protein, gene or complex. A complex is comprised of proteins, compounds, genes, other complexes, and any combination of these. We translated the annotations to a uniform identifier type, which is an Entrez Gene ID in case of proteins or genes, pubchem compound ID in case of compounds. Complexes are compared according to their individual protein or gene composition.

Relation

An interaction in which one or more entities is physically transformed into one or more other entities. Multi-step transformations, such as the relation of glucose to pyruvate in the glycolysis pathway, should be represented as pathways, if known.

Control

An interaction in which one entity regulates, modifies, or otherwise influences another. Two types of control interactions are defined activation and inhibition. In general, the targets of control processes should be interactions.

Biological Process

A biological process is a multi-step event, captured in a single node and often mediated by an entity. Biological processes are annotated with a GO Biological Process term.


Entity-level data modeling

Visualization Data Model

For visualization, we introduced the concept of "abstract node" to be compliant with the BioPAX entity concept. The abstract node can be a usual node, a pseudo node, or even a complex node. The pseudo node (gray circle) and complex node (red circle) can be used to describe aggregation of BAX, BCL2L1, and BCL2 to form a complex molecule. Our data model also supports activation (BAX) and translocation (CYCS) processes.