README.md

Bise Core Ontology

This repository hosts the core ontology of the BISE BioImaging Search Engine. Latest data dump is available from the bio.tools git hub: https://raw.githubusercontent.com/bio-tools/content/master/datasets/bise-ontology-biii-dump.ttl

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) :

• http://vowl.visualdataweb.org/webvowl-old/webvowl-old.html#iri=https://raw.githubusercontent.com/NeuBIAS/bise-core-ontology/master/owl-ontology/bise-core-ontology-v1.1.owl
• (broken link) http://www.essepuntato.it/lode/owlapi/https://raw.githubusercontent.com/NeuBIAS/neubias-data-model/master/owl-ontology/bise-core-ontology-v1.1.owl

Demo queries

demo-queries.md

Demo notebooks

• Example of advanced ontology-based queries :
• Quality-oriented queries :
• Authors network visualisation query:

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