togoid's Introduction

TogoID

Prerequsites

Installation

$ bundle exec rails g docker_compose --env=production
$ docker-compose up -d

$ docker-compose exec app bundle exec thor resource:fetch --dir /data/import hgnc
$ docker-compose exec app bundle exec thor resource:load --dir /data/import hgnc

### resource:fetch affymetrix is not yet implemented
$ docker-compose exec app bundle exec thor resource:load --dir /data/import affymetrix

Web API

Note: All your request URLs must be percent-encoded

ID conversion

Parameters

Key	Value
id `required`	Identifiers (comma or whitespace separated)
from	Input data source Detect automatically if no value specified
to	Output data source

Available data sources

Data source	Value	Pattern
HGNC Gene Symbol	hgnc
NCBI Gene ID	ncbi	`^\d+$`
RefSeq ID	refseq	`^(NC\|NG\|NM\|NR\|NT\|XM\|XR\|YP)_\d+$`
Affymetrix ID	affymetrix	`\d{4,}((_[asx])?_at)?`
Ensembl ID	ensg	`^ENSG\d{11}$`

Example

Convert single identifier

Request

GET /convert?id=ALDH1A1

Response

[
  {
    "source": {
      "id": "ALDH1A1",
      "type": "hgnc",
      "label": "HGNC"
    },
    "destination": [
      {
        "id": "216",
        "type": "ncbi",
        "label": "NCBI Gene"
      }
    ]
  }
]

Convert multiple identifier

Request

GET /convert?id=216%2C8854

Note: %2C is URL encoded string for comma

Response

[
  {
    "source": {
      "id": "216",
      "type": "ncbi",
      "label": "NCBI Gene"
    },
    "destination": [
      {
        "id": "ALDH1A1",
        "type": "hgnc",
        "label": "HGNC"
      }
    ]
  },
  {
    "source": {
      "id": "8854",
      "type": "ncbi",
      "label": "NCBI Gene"
    },
    "destination": [
      {
        "id": "ALDH1A2",
        "type": "hgnc",
        "label": "HGNC"
      }
    ]
  }
]