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aehrc/quickumls-rest

By aehrc

•Updated about 8 years ago

Ubuntu based image for running QuickUMLS rest service.

Image
2

839

aehrc/quickumls-rest repository overview

This project provides a Docker image for running QuickUMLS.

⁠Overview

The image contains a working install of QuickUMLS. In addition a lightweight REST wrapper is provided. This is main method for accessing QuickUMLS

⁠Setup

  1. First, download and install docker for your operating system.

  2. Pull the docker image from docker hub:

docker pull aehrc/quickumls-rest:1.2.3-2018AA

Replace 1.2.3-2018AA with a different tag if referred. Version is tied to QuickUMLS and UMLS version; hence, 1.2.3-2018AA represents QuickUMLS version 1.2.3 and UMLS version 2018AA.

⁠Running

The command to run is:

docker run -p 5000:5000 aehrc/quickumls-rest:1.2.3-2018AA

This will start the server and ensure that the listening port 5000 is mapped to 5000 on the host machine.

To run the contained in detached mode (in the background) run:

docker run -d -p 5000:5000 aehrc/quickumls-rest:1.2.3-2018AA

⁠Using the service

The service should now be running on localhost:5000.

The service accepts HTTP POST to localhost:5000/match with a JSON body containing a single text field; e.g.,:

{
  "text": "Fracture"
}

Which currently return an JSON array:

[
    {
        "cui": "C0016658",
        "end": 8,
        "ngram": "Fracture",
        "preferred": 1,
        "semtypes": [
            "T037"
        ],
        "similarity": 1,
        "snomed_ct": [
            "245384018",
            "120776011",
            "473534016",
            "537691016",
            "319350017",
            "403161016",
            "537785013",
            "245481010",
            "120777019",
            "402879010",
            "319349017",
            "319355010",
            "194093016",
            "329379013",
            "473535015",
            "450379018",
            "703674017",
            "773976012",
            "490930012",
            "813011010",
            "729455017",
            "594415012",
            "661921012",
            "594410019",
            "319348013",
            "603507019",
            "2726923019",
            "662170013",
            "2727632010",
            "2565056010",
            "2760272014",
            "2713761019",
            "2708851011"
        ],
        "start": 0,
        "term": "fracture"
    },
    {
        "cui": "C1963113",
        "end": 8,
        "ngram": "Fracture",
        "preferred": 1,
        "semtypes": [
            "T033"
        ],
        "similarity": 1,
        "snomed_ct": [],
        "start": 0,
        "term": "fracture"
    },
    {
        "cui": "C0016658",
        "end": 8,
        "ngram": "Fracture",
        "preferred": 1,
        "semtypes": [
            "T037"
        ],
        "similarity": 0.8571428571428571,
        "snomed_ct": [
            "245384018",
            "120776011",
            "473534016",
            "537691016",
            "319350017",
            "403161016",
            "537785013",
            "245481010",
            "120777019",
            "402879010",
            "319349017",
            "319355010",
            "194093016",
            "329379013",
            "473535015",
            "450379018",
            "703674017",
            "773976012",
            "490930012",
            "813011010",
            "729455017",
            "594415012",
            "661921012",
            "594410019",
            "319348013",
            "603507019",
            "2726923019",
            "662170013",
            "2727632010",
            "2565056010",
            "2760272014",
            "2713761019",
            "2708851011"
        ],
        "start": 0,
        "term": "fractures"
    }
]

⁠Building the Docker Image

This section describes how to build the Docker image. In most cases you will not need to do this. Note that versioning for the image is currently tied to the version of QuickUMLS used plus the version of UMLS used; hence, 1.2.3-2018AA represents QuickUMLS version 1.2.3 and UMLS version 2018AA.

  1. Copy the quickumls index, often called "quickumls_fp" into the same directory as the Dockerfile
  2. Build the image via docker build -t aehrc/quickumls-rest:1.2.3-2018AA . - note the . at the end. (replace 1.2.3-2018AA with relevant QuickUMLS and UMLS versions).
  3. Push to Docker hub via docker push aehrc/quickumls-rest:1.2.3-2018AA. (replace 1.2.3-2018AA with relevant QuickUMLS and UMLS versions).
⁠ChangeLog

v1.2.3-2018AA

  • Now supports mapping UMLS concepts to SNOMED_CT.

v1.2.3-2018AA

  • UMLS 2018AA and QuickUMLS v1.2.3
  • Now supports HTTP GET via http://host:port/word where word is the text to map.

v1.2.3

  • UMLS 2016AA and QuickUMLS v1.2.3

Tag summary

Content type

Image

Digest

Size

1.1 GB

Last updated

about 8 years ago

docker pull aehrc/quickumls-rest:1.2.3-2018AA