TopologyGraph

Overview

This is a description of the “topology” graphs used in GOlr. This document assumes that you are familiar with the JSON used in BBOP JS for graphs in general.

Answering a Question

By convention, there is a topology graph associated with documents types that are concerned with answering graph/ontology questions. The specific use of the topology_graph_json field is to:

• given a reference/topic node
• what are the all nodes and edges to the root(s)
• what are all nodes and edges for immediate children
• no other nodes or edges are given

The purpose is to give a good graph base for consuming widgets.

An Example

Given the above, let’s look at the topology graph for GO:004347. The topology_graph_json field would be:

{
    "edges": [
        {
            "pred": "is_a",
            "obj": "GO:0044699",
            "sub": "GO:0043473"
        },
        {
            "pred": "is_a",
            "obj": "GO:0044699",
            "sub": "GO:0044710"
        },
        {
            "pred": "part_of",
            "obj": "GO:0043473",
            "sub": "GO:0043474"
        },
        {
            "pred": "is_a",
            "obj": "GO:0044710",
            "sub": "GO:0042440"
        },
        {
            "pred": "is_a",
            "obj": "GO:0042440",
            "sub": "GO:0043474"
        },
        {
            "pred": "is_a",
            "obj": "GO:0008152",
            "sub": "GO:0044710"
        },
        {
            "pred": "is_a",
            "obj": "GO:0008150",
            "sub": "GO:0008152"
        },
        {
            "pred": "is_a",
            "obj": "GO:0043474",
            "sub": "GO:0046158"
        },
        {
            "pred": "is_a",
            "obj": "GO:0043474",
            "sub": "GO:0043324"
        },
        {
            "pred": "is_a",
            "obj": "GO:0008150",
            "sub": "GO:0044699"
        },
        {
            "pred": "is_a",
            "obj": "GO:0043474",
            "sub": "GO:0043475"
        }
    ],
    "nodes": [
        {
            "lbl": "single-organism metabolic process",
            "id": "GO:0044710"
        },
        {
            "lbl": "pigment metabolic process",
            "id": "GO:0042440"
        },
        {
            "lbl": "pigment metabolic process involved in pigment accumulation",
            "id": "GO:0043475"
        },
        {
            "lbl": "pigment metabolic process involved in developmental pigmentation",
            "id": "GO:0043324"
        },
        {
            "lbl": "single-organism process",
            "id": "GO:0044699"
        },
        {
            "lbl": "pigment metabolic process involved in pigmentation",
            "id": "GO:0043474"
        },
        {
            "lbl": "pigmentation",
            "id": "GO:0043473"
        },
        {
            "lbl": "metabolic process",
            "id": "GO:0008152"
        },
        {
            "lbl": "ocellus pigment metabolic process",
            "id": "GO:0046158"
        },
        {
            "lbl": "biological_process",
            "id": "GO:0008150"
        }
    ]
}