Name: biolink-api
Owner: biolink
Description: API for linked biological knowledge
Created: 2016-12-17 01:42:34.0
Updated: 2018-01-04 00:08:54.0
Pushed: 2018-01-10 00:03:29.0
Homepage: http://api.monarchinitiative.org/api/
Size: 834
Language: Python
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An API providing access to information on biologically and biomedically relevant entities, and the relationships between them, including:
This repository provides an example server for the biolink API. This can be customized for other sources; or an entirely new implementation conforming to the API can be created.
This API is designed to be implemented or partially implemented via a variety of databases.
The Monarch instance provides access to a wide variety of aggregated data:
http://api.monarchinitiative.org/api/
Note this instance also provides access to GO annotations.
After checking out this repo:
art-server.sh
This uses gunicorn and starts a server on 8888 by default. pyvenv is activated automatically.
Then look at:
http://localhost:8888/api/
For the swagger docs
To run in development mode:
nv venv
ce venv/bin/activate
install -r requirements.txt
rt PYTHONPATH=.:$PYTHONPATH
on biolink/app.py
See the swagger UI for more details. Click on 'model' under any of the routes.
The primary abstraction used in the modeling is the distinction between named objects and associations.
These examples are compiled from the behave tests
This is the repo:
https://github.com/biolink/biolink-api/
You can run a server instance locally with very little effort (less than one minute), see below:
This server implementation is primarily a flask-rest wrapper onto the ontobio package.
This API will wrap and integrate number of different more modular APIs and database engines or analysis services. The idea is that the API implementation will do the right thing - for example, using Solr for searches but injecting results with fast in-memory traversal of ontology graphs.
A service implementing the Biolink API can be accessed through standard http libraries. We also provide client language bindings, generated through swagger-codegen. For more information, see:
This is intended as a think wrapper layer, integrating existing services, as shown here: