python utilities for working with ontologies

This repo requires Python3.6 or later. See setup.py for additional requirements. ontload requires Java8 and >=maven3.3 in order to build SciGraph. parcellation.py requires FSL to be installed or you need to obtain the atlases in some other way.

In order to get good (deterministic) ttl serialization from these tools you need to use my modified version of rdflib (see RDFLib/rdflib#649). Follow the steps below in your preferred python environment. You may need to run pip install wheel.

1. Get a copy of the whl file for my release wget https://github.com/tgbugs/rdflib/releases/download/v5.0.0-dev-tgbugs-b1/rdflib-5.0.0_dev_tgbugs-py2.py3-none-any.whl
2. Install the whl pip install --user --upgrade rdflib-5.0.0_dev_tgbugs-py2.py3-none-any.whl
3. If you have not done so already git clone https://github.com/tgbugs/pyontutils
4. cd pyontutils && python 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. If you use a development setup you will need to create symlinks described below.

pyontutils provides a set of scripts that are useful for maintaining and managing ontologies using git, and making them available via SciGraph. Note that if you choose the development installation option you will need to ln -sT the scripts to your perferred bin folder.

1. ttlfmt Reserialize an ontology file using deterministic turtle (spec).
2. ontutils Various useful and frequently needed commands for ontology processes as well as less frequent refactorings.
3. ontload Load an ontology managed by git into SciGraph for easy deployment of services.
4. qnamefix Set qnames based on the curies defined for a given ontology.
5. necromancy Find dead ids in an ontology and raise them to be owl:Classes again.
6. scigraph-codegen Generate a rest client against a SciGraph services endpoint.
7. scig Run queries against a SciGraph endpoint from the command line.
8. ilxcli Given an ontlogy file with temporary identifiers, get persistent, resolvable identifers for them from InterLex.

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. ontload can be used to load your ontology into SciGraph for local use.

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. Please see the documentation for how to set up neuron-lang for jupyter notebooks and take a look at some examples of how to use neuron-lang to create new neurons.