README.md

UMLS suggestions

A compact search engine to suggest (preferred) UMLS terms.

Installation

This is a small nodeJS and elasticsearch project.

• Download UMLS : http://www.nlm.nih.gov/research/umls/
• Run the load scripts to get the UMLS records in database
• Add index keys to the mrconso and mrsty database (on CUI)
  • ALTER TABLE mrconso ADD INDEX(CUI);
  • ALTER TABLE mrsty ADD INDEX(CUI);
• npm install to get the node modules.
• cp json/example_config.json json/config.json to create a local config file. Edit this to the correct database settings.

Usage

If you have elasticsearch, node and npm installed you can use npm start (assuming elasticsearch runs on localhost:9200). There is now an app on localhost:9000. Since it is only a prototype there are no security settings. To setup your "database" goto: localhost:9000/install. This will create an empty index for new records.

After installing you can insert UMLS records. Enter the CUI + preferred title and alternatives. The alternatives can contain multiple entries seperated by |.

API

Request	Method	Response summary
/insert	GET	Form to insert an UMLS entry (CUI, Title and alternatives)
/insert	POST	Saves the UMLS entry and adds the alternatives as suggestions (i.e you create a mapping of alternatives to single CUI : TITLE format)
/	GET	Search form
/search	GET	Search form
/search	POST	Search for suggestions based on given query parameter. Returns a list of possible outcomes
/install	GET	Create the index and mapping for elasticsearch

Info

Elasticsearch database tutorial / getting started:

http://red-badger.com/blog/2013/11/08/getting-started-with-elasticsearch/