Towards defining a tree JSON format

README.md

Towards defining a (phylogenetic) tree JSON Format

After a fair bit of digging, I was unable to find a single, defined JSON structure for phylogenetic data. With awesome visualization libraries (like D3) emerging, I think it is necessary to standardize a JSON grammar to allow libraries like DendroPy to access such visualizations.

In this document, I attempt to define this set of rules and grammar.

Metadata Keys

name	meaning	type	required
name	name of the organism.	string	X
length	length of branch from parent to node	float
childen	array of children nodes	array
id	free id to be used by any program	string
accver	NCBI accession number	string
sequence	raw sequence	string
taxonomy	sub-JSON tree of taxonomy	JSON object
score	score at node	float

Visualization Keys

name	meaning	type	required
color	name of the organism.	string
label	node label for visualization	string

Rules

tree.json

{
  "name": "root",
  "children": [{
    "name": "child1",
  }, {
    "name": "child2",
    "children":[{
      "name": "child1-1",
    },{
      "name": "child1-2",
    }],
  }, {
    "name": "child3",
  }]
}