callahantiff / PheKnowLator

PheKnowLator: Heterogeneous Biomedical Knowledge Graphs and Benchmarks Constructed Under Alternative Semantic Models

https://github.com/callahantiff/PheKnowLator/wiki

Apache License 2.0

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Maintenance #136

Closed callahantiff closed 1 year ago

callahantiff commented 1 year ago

Purpose

This PR provides some very basic maintenance needed to clean address some errors in the OWL-NETS pipeline, clean up typos in docstrings, remove pkt bnodes from fully processed OWL graphs, and address deprecated functions in NetworkX.

Scripts Impacted

owlnets.py.
- Updated to fix the prior bad assumption about classes and axioms built using UnionOf constructors
metadata.py
- Removed dependency on read_gpickle and write_gpickle as these have been deprecated in NetworkX v3.0 (details here)

Data Sources/Documentation Impacted

For OWL graphs, we allow the logic only and annotation only subsets to contain pkt-namespaced bnodes, but remove the pkt namespace from full owl file.

Notebooks Impacted

OWLNETS_Example_Application.ipynb
Entity_Search.ipynb

Other Updates

The following Wiki pages have been updated:
- v2-Data-Sources
- Updated to included better descriptions
- KG Construction
- Section describing the KG output has been updated to note that all output are g-zipped
- OWL-NETS 2.0
- Section describing the KG output has been updated to note that all output are g-zipped

Associated Issues

137

sonarcloud[bot] commented 1 year ago

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities
0 Security Hotspots
4 Code Smells

89.8% Coverage
0.0% Duplication