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KG-Hub

A collection of biological and biomedical Knowledge Graphs, including their component data sources.

Learn more about KG-Hub

Build your own KG

Purpose

The purpose of Knowledge Graph Hub (KG Hub) is to provide a platform for building knowledge graphs (KGs) by adopting a set of guidelines and design principles.

The goal of KG Hub is to serve as a collective resource to simplify the process of generating biological and biomedical KGs and thus reducing the barrier for entry to new participants.

In a KG Hub, each independent effort for building a KG is an instance of the KG Hub.

For example, KG-COVID-19, a light-weight ETL framework for building a COVID-19 KG, is an instance of KG Hub.

Design Principles

  • Each instance of KG Hub,
  • should live in its own GitHub repository within the Knowledge-Graph-Hub organization.
  • should have code and/or configurations for Extract, Transform, and Load (ETL) and must be reproducible.
  • should do their best to model their data using the Biolink Model, where possible.
  • should make use of ontologies from the OBO Foundry, where possible.
  • should be responsible for the veracity of the datasets that they ingest and are responsible for keeping track of evidence and provenance for assertions in their KG.
  • should provide their KG for download and must follow semantic versioning guidelines.
  • should provide their KG in the KGX interchange format in addition to their format of choice.
  • must have a License, Contributing guidelines, Code of Conduct, and be open to the community for contributions as well as consumption.

Optionally, each instance of a KG Hub can also provide a Docker image such that their code can be run easily as a container.

KG-Hub Projects

The table below lists active KG projects. Click headings to sort.

id description url repository former_id
kg-obo KG-OBO: OBO ontologies into KGX TSV format. https://kghub.io/kg-obo/ https://github.com/Knowledge-Graph-Hub/kg-obo nan
kg-idg KG-IDG: a Knowledge Graph for Illuminating the Druggable Genome. https://kghub.io/kg-idg/ https://github.com/Knowledge-Graph-Hub/kg-idg nan
kg-covid-19 KG-COVID-19: a knowledge graph for COVID-19 and SARS-COV-2. https://kghub.io/kg-covid-19/ https://github.com/Knowledge-Graph-Hub/kg-covid-19 nan
kg-microbe KG-Microbe: a knowledge graph for microbial traits. https://kghub.io/kg-microbe/ https://github.com/Knowledge-Graph-Hub/kg-microbe nan
eco-kg eco-KG: a knowledge graph of plant traits starting with Planteome and EOL TraitBank. https://kghub.io/eco-kg/ https://github.com/Knowledge-Graph-Hub/eco-kg nan
monarch Graph representation of the Monarch Initiative knowledge resource. https://kghub.io/kg-monarch/ https://github.com/monarch-initiative nan
kg-phenio Graph representation of Monarch ontologies. https://kghub.io/kg-phenio/ https://github.com/Knowledge-Graph-Hub/kg-phenio kg-ontoml
sldb A graph of synthetic lethal interactions. https://kghub.io/sldb/ https://github.com/monarch-initiative/SLDBGen nan
rna-kg A graph integrating knowledge about human RNAs. A preprint describing this project is here https://github.com/AnacletoLAB/RNA-KG https://github.com/AnacletoLAB/RNA-KG nan
kg-enp Experimental natural products knowledge graph. https://enpkg.commons-lab.org/ https://github.com/AnacletoLAB/RNA-KG nan