vocab-service

Vocab Service

This is a simple service for querying vocabulary classes extracted from the Bioportal. Since many vocabularies are hierarchical, Neo4j is used as the database to store and query the classes.

Install

Requires Go to install, however if you want pre-built binaries please request it!

go get github.com/chop-dbhi/go-bioportal/cmd/vocab-service

Usage

It requires a connection to a Neo4j server through the Bolt interface. The address defaults to the default Bolt address bolt://127.0.0.1:7687. If authentication is required, the <user>:<password> parts of the URI must be supplied.

vocab-service [-http] [-neo4j] [-tlscert] [-tlskey]

Methods

Below are list of the methods the service supports.

• Get(vocab, class) - Get the details of a class in the target vocabulary.
• Validate(vocab, classes)- Validate the set of classes are in the vocabulary.
• Match(vocab, pattern) - Perform a pattern match on the label of the class.
• Parents(vocab, class) - Get the parents of the class.
• Children(vocab, class) - Get the children of the class.
• Ancestors(vocab, class) - Get all ancestors of the class.
• Descendants(vocab, class) - Get all descendants of the class.
• Flatten(vocab, classes) - Flatten the hierarchy for all classes passed.

Interfaces

HTTP

A request is a POST with a JSON-encoded body with the following structure. The keys of the the params entry correspond to the parameter names in the method signatures.

{
  "method": "match",
  "params": {
    "vocab": "icd10cm",
    "pattern": "down syndrome.*"
  }
}