The entire “data.imicrobe.us” is accessible programmatically via our REST API.

Available endpoints

A list of available endpoints can be found at http://data.imicrobe.us/index.json (or s/json/txt/). As of Dec 2014, they include:

  • /assembly/info
  • /assembly/list
  • /assembly/view/:assembly_id
  • /combined_assembly/info
  • /combined_assembly/list
  • /combined_assembly/view/:combined_assembly_id
  • /index
  • /info
  • /project/browse
  • /project/info
  • /project/list
  • /project/view/:project_id
  • /project_page/info
  • /project_page/view/:project_page_id
  • /pubchase/info
  • /pubchase/list
  • /publication/info
  • /publication/list
  • /publication/view/:publication_id
  • /reference/info
  • /reference/list
  • /sample/info
  • /sample/list
  • /sample/view/:sample_id
  • /search
  • /search/info

Each “info” endpoint provides instructions about the other actions available, e.g.:

curl -s -H "Accepts: application/json" http://data.imicrobe.us/project/info.json | jq '.'
{
  "list": {
    "params": {
      "domain": {
        "type": "str",
        "desc": "a domain of life to which projects belong",
        "required": "false"
      }
    },
    "results": "a list of combined assemblies"
  },
  "view": {
    "results": "the details of a project",
    "params": {
      "project_id": {
        "type": "int",
        "required": "true",
        "desc": "the project id"
      }
    }
  },
  "browse": {
    "results": "a list of the number of projects associated with a domain of life"
  }
}

Examples

You can get a list of assemblies in JSON format by requesting:

http://data.imicrobe.us/assembly/list.json

Where a field is preceded with a colon, e.g., “/assembly/view/:assembly_id,” you must substitute the integer value of the “assembly_id”:

http://data.imicrobe.us/assembly/view/1.json

Change the “.json” to “.txt” to see a different textual representation:

http://data.imicrobe.us/assembly/view/1.txt