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NPM version

Translate OBO Graphs into Dot/Graphviz

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

Requirements

  • Node.js ≥ 14.16

Installation

The obographviz package can be installed via NPM either locally or globally. If you're not familiar with NPM, see the following to get started:

If you intend to primarily use the command line tool provided by this package or you're using a tool like Ontology Access Kit which depends on it, install globally:

npm install -g obographviz

Once installed globally, the og2dot executable will automatically be added to your PATH.

Otherwise, if you want to use the package in an existing Node.js project install it locally:

npm install obographviz

Quickstart

Command line

All examples in this README assume obographviz has been installed globally. If it was installed locally to a project, call og2dot via npx or an npm script.

See the examples directory in this repositories for sample OBO Graph JSON files and stylesheets.

og2dot simple-og.json > test.dot
dot test.dot -Tpng -Grankdir=BT > test.png

API

import { OboGraphViz } from "obographviz";

const obograph = { ... }

const compoundRelations = ['BFO:0000050']
const styleMap = {}
const gv = new OboGraphViz(obograph)
const dot = gv.renderDot(compoundRelations, styleMap)
console.log(dot)

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:

og2dot -c is_a simple-og.json > test.dot

Generates:

img

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.

og2dot -s example-style.json -c is_a 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 -s uberon-style.json digit.json -t png -o digit.png

Renders:

img

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 -s uberon-zfa-style.json uberon-zfa-xref-example.json -t png -o uberon-zfa-xref-example.png

Renders:

img

(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"
}
og2dot -c BFO:0000050 -c RO:0002333 -s gocam-style.json lego-example2.json

img

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
            }
        ]
    }
}

Ontology Access Kit

This library is integrated into Ontology Access Kit (OAK) to support its viz subcommand. For example:

runoak -i ontobee: viz HP:0000787

This proceeds by:

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

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.

Development

Javascript and TypeScript files in the lib directory are compiled using tsc into the dist directory. To compile once use:

npm run build

To watch for file changes and compile incrementally use:

npm run dev

Before committing changes run the test suite with:

npm test

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