CROssBAR-BioCypher-Migration

This is a repo for CROssBARv2 data to the Neo4j database via BioCypher. CROssBARv2 is, an extended and improved version of our previous work (for v1 please check CROssBAR), a heterogeneous general purpose biomedical knowledge graph (KG) based system.

This repo is currently under development. Therefore, you may encounter some problems while replicating it. Feel free to open issue if you encounter any problems.

Installation

The project uses Poetry. You can install like this:

git clone https://github.com/HUBioDataLab/CROssBAR-BioCypher-Migration.git
cd CROssBAR-BioCypher-Migration
poetry install

Poetry will create a virtual environment according to your configuration (either centrally or in the project folder). You can activate it by running poetry shell inside the project directory.

Note about pycurl

You may encounter an error when executing the UniProt adapter about the SSL backend in pycurl: ImportError: pycurl: libcurl link-time ssl backend (openssl) is different from compile-time ssl backend (none/other)

Should this happen, it can be fixed as described here: https://stackoverflow.com/questions/68167426/how-to-install-a-package-with-poetry-that-requires-cli-args by running poetry shell followed by pip list, noting the version of pycurl, and then running pip install --compile --install-option="--with-openssl" --upgrade --force-reinstall pycurl==<version> to provide the correct SSL backend.