LabOP / SiLA Device Databank and Ontology

This project provides a infrastructure for the development of an open ontology for scientific device.

It further develops a microservice that provides a SPARQL endpoint for querying the device ontology and a SiLA 2.0 server that can be addressed, e.g. by lab-automation tasks.

Potential use cases for the ontology are:

• Device management : e.g. a device can be stored in a device management system
• Device identification : e.g. a device can be identified by a barcode
• Device tracking : e.g. a device can be tracked through the different steps of an experiment
• Device documentation: e.g. a device can be documented with a picture, a description, a link to a protocol, etc.
• Device interoperability: does a certain device fit into a certain instrument? does a certain lid fit onto a certain tube?
• Device automation: e.g. liquid handling robots
• Device recommendation: a LIMS system can recommend device based on the desired experiment

This is a shared project between the LabOP project and the SiLA 2.0 working group project.

Features

• Device Ontology
• SPARQL endpoint for querying the device ontology (including a web interface)
• SiLA 2.0 compliant endpoint for querying the device ontology

Usage

Installation

With docker-compose:

 wget https://raw.githubusercontent.com/Bioprotocols/device-databank/main/docker/docker-compose.yml
 # or with curl:
 curl -O https://raw.githubusercontent.com/Bioprotocols/device-databank/main/docker/docker-compose.yml

 # to pull the docker containers from the github container registry, run in the directory where the docker-compose file is located:
 docker-compose pull

 # to start the docker containers, run in the directory where the docker-compose file is located (add -d to run in the background):
 docker-compose up

Now you can access the SPARQL endpoint web interface at localhost:8008.

The jupyter-lab notebook is available at localhost:8009. The default password for the jupyter server is device.

The SiLA 2.0 server listens at localhost:50052.

Access using the SPARQL endpoint with curl

   curl -X POST -H "Content-Type: application/sparql-query" -H "Accept: application/sparql-results+json" --data "SELECT * WHERE { ?s ?p ?o } LIMIT 10" http://localhost:8008/sparql
    curl --header "Accept: application/sparql-results+json"  -G 'http://localhost:8008/sparql' --data-urlencode query='
SELECT ?s WHERE {
 ?s ?p ?o
} LIMIT 10'

Access using the SiLA 2.0 server

We provided some examples of how to access the ontology using the SiLA 2.0 server. You can find them in the examples folder. For the ease of playing with the SiLA 2.0 server, we also provide a jupyter-lab notebook with some examples. You can find it in the jupyter folder.

Documentation

The Documentation can be found here: openlab.gitlab.io/labop-device-ontology or labop-device-ontology.gitlab.io

Credits

This package was created with Cookiecutter* and the opensource/templates/cookiecutter-pypackage* project template.

Cookiecutter opensource/templates/cookiecutter-pypackage