floor3d / nameresolution

A service for finding CURIEs from lexical strings.

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

docker run --name name_lookup -d -p 8983:8983 -t solr -DzkRun
docker run -it -v /local/NameResolution/data:/json -v /projects/datatrans/synonyms/March17_2021/:/csv -v /local/NameResolution:/NameResolution python:3.9 bash
    ./csv2json.py /csv/anatomy.txt_synonyms.txt /json --sep "\t"
./setup.sh "/local/NameResolution/data/*.json"

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"