Name resolution service

This service takes lexical strings and attempts to map them to identifiers (curies) from a vocabulary or ontology.
The lookup is not exact, but includes partial matches.

Multiple results may be returned representing possible conceptual matches, but all of the identifiers have been correctly normalized using the NodeNormalization service.

See the documentation notebook for examples of use.

Docker setup

docker-compose up

native setup

Solr database

See instructions in the data-loading/ directory.

API

pip install -r requirements.txt
./main.sh

Kubernetes

Helm charts can be found at https://github.com/helxplatform/translator-devops/helm/r3

examples

curl -X POST "http://localhost:6434/lookup?string=oxycod&offset=0&limit=10" -H "accept: application/json"

Configuration

NameRes can be configured by setting environmental variables:

• SOLR_HOST and SOLR_PORT: Hostname and port for the Solr database containing NameRes information.
• SERVER_NAME: The name of this server (defaults to infores:sri-name-resolver)
• SERVER_ROOT: The server root (defaults to /)
• MATURITY_VALUE: How mature is this NameRes (defaults to maturity, e.g. development)
• LOCATION_VALUE: Where is this NameRes setup (defaults to location, e.g. RENCI)
• OTEL_ENABLED: Turn on Open TELemetry (default: 'false') -- only 'true' will turn this on.
  • JAEGER_HOST and JAEGER_PORT: Hostname and port for the Jaegar instance to provide telemetry to.
  • JAEGER_SERVICE_NAME: The name of this service (defaults to the value of SERVER_NAME)