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Bise Core Ontology

This repository hosts the core ontology of the BISE BioImaging Search Engine.

Ontology development process

  1. Web protégé (online web editor) : https://webprotege.stanford.edu/#projects/38b3da5d-b5ce-4d59-972c-23fcb700256a
  2. Export to an OWL file
  3. Documentation generation (LODE) :

Demo queries

demo-queries.md

Demo notebooks

  • Example of advanced ontology-based queries : Binder
  • Quality-oriented queries : Binder

Getting python dependencies

With Conda :

conda create --name bise-ld-webapp
source activate bise-ld-webapp
conda install rdflib jupyter -c conda-forge

Or with pip :

pip install rdflib
pip install jupyter

Launching the notebook

jupyter-notebook

Demo web app

Virtual environment setup to get python dependencies

conda create --name bise-ld-webapp
source activate bise-ld-webapp
conda install flask rdflib pymongo -c conda-forge
conda install rdflib-jsonld -c bioconda

Launch the web app

cd bise-linked-data-webapp
python app.py

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