Translate OBO Graphs into Dot/Graphviz

• Input: a OBO Graph JSON object
• Optional: a JSON ontology stylesheet
• Output: a Dot-format / Graphviz file

Quickstart

Command line:

./bin/og2dot.js tests/simple-og.json > test.dot
dot test.dot -Tpng -Grankdir=BT > test.png

Command line; from python obographs package

ogr -p subClassOf BFO:0000050 -r obo:go -t png g nucleus

API:

    var compoundRelations = ['BFO:0000050']
    var styleMap = {}
    var gv = new ogv.OboGraphViz(result.data)
    var dot = gv.renderDot(compoundRelations, styleMap)

Features

Nesting

One or more predicates can be designated as 'compound', i.e. used for nesting.

On the command line, use -c. In the API, use compoundRelations

Example:

./bin/og2dot.js -c is_a tests/simple-og.json > test.dot

Generates:

Note only works for subgraphs that exhibit disjointness over this property, acyclicity

Use the -I option for inverting the containment relation (e.g. to use has part rather than part of).

Stylesheets

In the API can be passed using styleMap. On the command line, by using either -s (to pass a JSON file) or -S (to pass stringified JSON object directly on command line)

E.g.

./bin/og2dot.js -s examples/example-style.json -c is_a tests/simple-og.json > test.dot

Stylesheet Standard

This is now documented separately:

kgviz-model

Global stylemap properties

These go in the root of the stylemap object

{
    "style": "filled",
    "fillcolor": "green"
}

this sets all nodes to be filled green

Edge properties by relationship type

Each relationship type can have its own individual style, by passing relationProperties. This is keyed by the CURIE for the relation (or "is_a" for subClassOf):

{
    "relationProperties": {
        "is_a": {
            "color": "black",
            "penwith": 3,
            "arrowhead": "open",
            "label": ""
        },
        "BFO:0000050": {
            "arrowhead": "tee",
            "color": "blue"
        }
    }
}

Node properties by prefix

Pass in prefixProperties to be able to assign individual properties for ontology prefixes. This can be useful when visualization graphs that combine multiple ontologies

{
    "prefixProperties": {
        "SO": {
            "fillcolor": "yellow"
        },
        "RO": {
            "fillcolor": "pink"
        },
        "BFO": {
            "fillcolor": "cyan"
        }
    }
}

Conditional properties

Arbitrary conditions can be set using conditionalProperties for example:

{
    "conditionalProperties": [
        {
            "conditions": {
                "subset":"efo_slim"
            },
            "properties": {
                "fillcolor": "blue"
            }
        }
    }
}

This will color any node in the efo_slim subset blue.

Combined Example

The following example uses all subclasses of digit in Uberon, plus their ancestors, which forms a complex lattic structure.

See digit.json for the underlying ontology. See examples/uberon-style.json for the stylesheet.

og2dot.js -s examples/uberon-style.json examples/digit.json -t png -o examples/digit.png

Renders:

Nesting of Equivalence Sets

Optionally, cliques of classes interconnected with either equivalence axioms or xrefs will be clustered.

The file uberon-zfa-xref-example.json contains a subset of both UBERON, ZFA, and two Allen brain ontologies, with UBERON classes xref-ing equivalent ZFA classes.

og2dot.js -s examples/uberon-zfa-style.json examples/uberon-zfa-xref-example.json -t png -o examples/uberon-zfa-xref-example.png

Renders:

(Uberon: yellow, ZFA:black, MBA: pink, HBA: grey, black lines = IS_A, blue lines = part_of, equivalence sets as bounding boxes)

The predicates used to build these can be configured in the json style file, e.g.:

    "cliqueRelations": [
        "xref", "equivalent_to", "same_as"
    ]

Note: to style the bounding box in a stylesheet, the cliques are considered to be in the ID space %CLIQUE

    "prefixProperties": {
        "%CLIQUE": {
            "fillcolor": "hotpink"
        },
        "GO": {
            "fillcolor": "yellow"
        },

Rendering anonymous and pseudo-anonymous individuals

E.g. GO-CAM models

{
 nodeFilter : {
                "type" : "INDIVIDUAL"
              },
              labelFrom : "type"
}

./bin/og2dot.js  -c BFO:0000050 -c RO:0002333 -s examples/gocam-style.json tests/lego-example2.json

Integration with other components

Configuring individual nodes or edges

As well as configuring via style sheets, an individual node or edge can configure its display by using an annotation assertion with a property in https://w3id.org/kgviz/, e.g.:

{
      "sub": "GO:0031090",
      "pred": "BFO:0000050",
      "obj": "GO:0043227",
      "meta": {
        "basicPropertyValues": [
          {
            "pred": "https://w3id.org/kgviz/penwidth",
            "val": 10
          }
        ]
      }
    }

Obographs python

See:

https://github.com/biolink/biolink-api/tree/master/obographs

(note: this python API may move to its own repo in future)

obographs-python command line:

ogr -p subClassOf BFO:0000050 -r go -t png   a nucleus

This proceeds by:

1. Using the python obographs library to extract a networkx subgraph around the specified node
2. Write as obographs-json
3. Calls og2dot.js

Use from biolink-api REST

Go to http://api.monarchinitiative.org/api/

See the /ontol/subgraph/ route

This exports obographs which can be fed in to this js lib

TODO - link to demo site

Use with AmiGO

AmiGO uses bbop-graphs; these are similar enough that they can be passed in instead of obographs.

FAQ

Why Dot/GraphViz?

Why not D3, cytoscape js etc?

These are all very nice and pretty, but GraphViz has some powerful features that I have not found in any other framework (or have been too lazy to find out how to do). In particular:

• Easy to run on command line
• The ability to nest relationships (update: compound graphs in cytoscape.js)
• simple control over box and edge visual attributes
• embedding arbitrary HTML

This is intended to replace blipkit graphviz generation. For some examples, see mondo report