Quick Start¶
git clone https://github.com/Knowledge-Graph-Hub/kg-obo
cd kg-obo
python3 -m venv venv && source venv/bin/activate # optional
pip install .
python run.py --bucket [your s3 bucket]
Overview¶
run.py iterates through ontologies found in this YAML file, checks whether an existing transform for each ontologies exists on the target s3 bucket directory using the tracking.yaml file, and if not transforms the ontology from OWL to KGX TSV, and puts the KGX nodes/edges TSV files up on the bucket at: s3_bucket/[target directory]/[ontology name]/[version]/
tracking.yaml file: OBO to Node/Edge Transform Tracking The OBO to Node/Edge Transform Tracking (tracking.yaml) file is used to keep track of current and previous version of transformed ontologies.
Each entry, named by its OBO ID, must contain the following:
- ‘current_iri’: the most recent version of the ontology, expressed as a full IRI, e.g.,
- ‘current_version’: the most recent version of the ontology, expressed as a version string, e.g.,
2019-08-26
The following two items may not exist if only one version is available:
‘archive_iris’: previous versions of the ontology, expressed in the format of ‘current_iri’.
‘archive_versions’: previous versions of the ontology, expressed in the format of ‘current_version’.
Download ontologies in KGX format¶
OBO ontologies transformed into are available here:
https://kg-hub.berkeleybop.io/kg-obo/
See here for a description of the KGX TSV format
git clone https://github.com/Knowledge-Graph-Hub/kg-obo
cd kg-obo
python3 -m venv venv && source venv/bin/activate # optional
pip install .
python3 run.py --bucket [your s3 bucket]
Contributors¶
Acknowledgements¶
We gratefully acknowledge the OBO community and thank all participants for making their data available.