PheKnowLator **DON'T MERGE -- ARCHIVE ** Build overhaul v4.0.0

DON'T MERGE -- ARCHIVE Build overhaul v4.0.0

Open callahantiff opened this issue 2 years ago • 1 comments

🛑 DO NOT USE THIS BRANCH OR MODIFY THIS PR -- CONTENT IS KEPT FOR NOTES 🛑

Purpose

This PR addresses several issues and overhauls many aspects of the current build, which is described in more detail below. The primary changes made impact the amount, type, and storage of metadata at both the node- and triple-level.

Issues Addressed by PR

#97
#99
#107
#114

Scripts Impacted

owlnets.py.
- Updated to fix the prior bad assumption about classes and axioms built using UnionOf constructors
metadata.py
- Get new functionality for processing Biolink types
edge_list.py
- Get new functionality for adding Bioregistry identifiers
utils/data_utils.py
- functions created to facilitated with API-access to BioLink and Bioregistry

Data Sources/Documentation Impacted

edge_source_list.txt
- Added back chemical-rna edge data
resource_info.txt
- Updated metadata for many of the edges, most often in an effort to soften the initial formatting that was applied to the data (i.e., having a more liberal and inclusive build, but providing the user with the ability to enforce specific filtering choices)
added back information for the chemical-rna edge

Notebooks Impacted

OWLNETS_Example_Application.ipynb
Data_Preparation.ipynb

Output Impacted

All output files will be g-zipped in order to improve resource use

Other Updates

The following Wiki pages have been udated:
- 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