The Biolookup Service is built on Flask
as a thin wrapper around the biolookup
Python package. It exposes a single endpoint for accessing entity metadata for which Swagger
API documentation is automatically generated
by Flasgger.
See the remaining Biolookup Service API documentation or follow this example for getting metadata for a given CURIE in Python:
import requests
res = requests.get("http://biolookup.io/api/lookup/doid:14330").json()
assert res["name"] == "Parkinson's disease"
assert res["identifier"] == "14330"
assert res["prefix"] == "doid"
assert res["definition"] is not None # not shown for brevity
The Python source code can be found at
biopragmatics/biolookup.
It can be installed with pip install biolookup or in development mode by following
these instructions.
The biolookup Python package can be used to interact with the web service or directly with the
database if it's pre-configured.
import biolookup
res = biolookup.lookup("doid:14330")
assert res["name"] == "Parkinson's disease"
assert res["identifier"] == "14330"
assert res["prefix"] == "doid"
assert res["definition"] is not None # not shown for brevity
As the biolookup package is open source, it's possible to host your own instance of the Biolookup
Service. Further, it's possible create a local derivative of the database with a custom instance of the Bioregistry. Here are examples how to do that:
You can also install and run the Biolookup Service from the shell:
$ pip install biolookup
$ biolookup webYou can also download the source code, install in development mode, and run the Biolookup Service from the shell:
$ git clone https://github.com/biopragmatics/biolookup.git
$ cd biolookup
$ pip install --editable .
$ biolookup webYou can deploy your own instance of the Biolookup Service with:
$ docker run -id -p 8765:8765 biopragmatics/biolookup:latestIf you want to load a custom database with a Docker-based deployment, please see the dockerfile in biopragmatics/biolookup-docker for inspiration.