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snomed-groovy

Groovy script to load snomed data into a neo4j container

Prerequistes: You need to install

  • Neo4j at port location: "bolt://localhost:7687", userName: "neo4j", password: "neo4j or what ever you have".Change it in ApplicationProperties
  • Install elastic search at the default port

** To start the upload => run Start.groovy

As Neo4j does not index the text, we are using elastic search to index the text and use the conceptId to zero in on a node in Neo4j. Once we and on a node we can navigate tthrough the graph to get the required data and relationships.

Create a simple to setup - set of docker container to populate snomed-ct data into the Neo4j Database.

This code does the following

  • Read the snomed description file and create a mapping between the concepts and

    • FSN
    • Synonym
    • Description
  • Create a list of Relationship types. To be used to add labels for relationships between nodes.

  • In the initial run create concepts with FSA, list of synoyms and descriptions.

  • In the third run setup the relationships between the concepts.

  • Each of the Concept and Relationship will be indexed both on the description text as well as the Label.

  • Concepts will have a "Concept" label.

  • Relationship will have a specific relationship label.

  • Use elastic search to make the nodes and relationships searchable by text.

MVP:

Get a Neo4j Database populated with SNOMED-CT international version. (/)

Nice to have:

Add an automcomplete, fuzzy search functionality => Created an Elastic search instance with neo4j data. Update uploaded nodes with Reference sets data.

Next Release:

Restful services to access SNOMED-CT data

  • Medications Resource
  • Problems List Resource
  • Allergies Resource
  • Diseases Resource

Also Map ICD to Snomed-Ct and LOINC to Snomed-CT expressions.

For a Python version of the same please have a look at https://github.com/pradeepvemulakonda/Snomed

For more information on SNOMED-CT and understand about Medical Terminology go to http://www.vemulakonda.com/2017/05/understanding-snomed-ct-data-model.html

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