/kegg-kg-converter

A simple data ingested using url constructors

Primary LanguageJupyter NotebookBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

Download-Transform-Merge Template

KG hub template for tools to generate knowledge graphs for projects

Documentation

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.

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

The merge.yaml shows merging of the various KGs.

Implementation

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

Setup

python setup.py install and python -m pip install -r requirements.txt