Use with external endpoint

AskOmics can be use to explore external endpoint such as NeXtProt.

Build external endpoint abstraction

First, build AskOmics abstraction of the external enpoint with Abstractor.

Install Abstractor in a python virtual env

# Create and source venv
python3 -m venv venv
source venv/bin/activate
# Install Abstractor
pip install abstractor

Generate AskOmics abstraction. The tool explore the entire endpoint, so it can be long.

# Need help ?
abstractor -h
# Generate abstraction
abstractor -e <enpoint_url> -p <main_prefix> -o abstraction.ttl

Deploy AskOmics

Deploy AskOmics with a special configuration to use it with an external endpoint. The following ini entry have to be updated:

  • askomics
    • disable_integration: true
  • triplestore
    • external_endpoint: <endpoint_url>
    • prefix = <main_prefix>
    • namespace = <main_prefix>

Integrate external endpoint

Create an account on the AskOmics instance. The first account is an admin account who can integrate datasets. Load the asbtraction.ttl and integrate it has a public dataset.

Other users can’t integrate datasets, but they can explore the external endpoint.