KG hub template for tools to generate knowledge graphs for projects

This template could be used for data ingestion for varied sources.

Components

• Download: The download.yaml contains all the URLs for the source data.
• Transform: The transform_utils contains the code relevant to trnsformations of the raw data into nodes and edges (tsv format)
• Merge: Implementation of the 'merge' function from KGX using merge.yaml as a source file.

Utilities

The code for these are found in the utils folder.

• NLP using OGER
• ROBOT for transforming ontology.OWL to ontology.JSON

Examples Included

Thes examples have download links and transform codes from other projects.

• Drug Central: Sampled from kg-covid-19. Code located here
• Ontology: Sampled from kg-covid-19. Code located here
• Traits: Sampled from kg-microbe. Code located here
• Example Transform: Boilerplate code for transforms. Code located here.

The merge.yaml shows merging of the various KGs. In this example we have ENVO, CHEBI, NCBITaxon and the Traits KGs merged.

Implementation

Use this template to generate a template in the desired repository and then refactor the string project_name in the project to the desired project name.