how to encode this data to parent / children structure in JSON

Question

I am working with d3.js to visualise families of animals (organisms) (up to 4000 at a time) as a tree graph, though the data source could just as well be a directory listing, or

Answer 1

Given your starting input I believe something like the following code will produce your desired output. I don't imagine this is the prettiest way to do it, but it's what came to mind at the time.

It seemed easiest to pre-process the data to first split up the initial array of strings into an array of arrays like this:

[
   ["Hemiptera","Miridae","Kanakamiris" ],
   ["Hemiptera","Miridae","Neophloeobia","incisa" ],
   //etc
]

...and then process that to get a working object in a form something like this:

  working = {
       Hemiptera : {
           Miridae : {
              Kanakamiris : {},
              Neophloeobia : {
                  incisa : {}
              }
           }
       },
       Lepidoptera : {
           Nymphalidae : {
              Ephinephile : {
                  rawnsleyi : {}
              }
           }
       }
    }

...because working with objects rather than arrays makes it easier to test whether child items already exist. Having created the above structure I then process it one last time to get your final desired output. So:

// start by remapping the data to an array of arrays
var organisms = data.organisms.map(function(v) {
        return v.name.split(".");
    });

// this function recursively processes the above array of arrays
// to create an object whose properties are also objects
function addToHeirarchy(val, level, heirarchy) {
    if (val[level]) {
        if (!heirarchy.hasOwnProperty(val[level]))
            heirarchy[val[level]] = {};
        addToHeirarchy(val, level + 1, heirarchy[val[level]]);
    }
}
var working = {};    
for (var i = 0; i < organisms.length; i++)
    addToHeirarchy(organisms[i], 0, working);

// this function recursively processes the object created above
// to create the desired final structure
function remapHeirarchy(item) {
    var children = [];
    for (var k in item) {
        children.push({
            "name" : k,
            "children" : remapHeirarchy(item[k])
        });
    }
    return children;
}

var heirarchy = {
    "name" : "ROOT",
    "children" : remapHeirarchy(working)
};

Demo: http://jsfiddle.net/a669F/1/