python utilities for working with ontologies
In order to get good (deterministic) ttl serialziation from these tools you need to use my modified version of rdflib (pull request submitted to upstream with a bit of work left to do).
Follow the steps below in your preferred python environment. You may need to run pip install wheel.
git clone https://github.com/tgbugs/rdflib.git && cd rdflib && python3 setup.py bdist_wheel && pip3 install --user --upgrade dist/rdflib*.whl- If you have not done so already
git clone https://github.com/tgbugs/pyontutils cd pyontutils && python3 setup.py bdist_wheel && pip3 install --user --upgrade dist/pyontutils*.whl
Alternately, if want a development setup or need to use these tools for working directly
with the NIF-Ontology repo you can add this folder to your PYTHONPATH environment
variable using export PYTHONPATH=PYTHONPATH:"$(pwd)" from the location of this readme.
This repo requires Python3.5 or later. See setup.py for the additional requirements.
Many of these scripts are written for working on the NIF standard ontology found here.
scigraph.py is code geneator for creating a python client library against a SciGraph REST endpoint. scigraph_client.py is the client library generated against the nif development scigraph instance.
If you have found your way to this repository because you are interested in using neuron-lang for
describing neuron types please see this wiki page.
To get started all you need to do is follow the installation instructions above and then include
from pyontutils.neuron_lang import * in your import statements. More documentation is coming soon.