KG-Hub
A collection of biological and biomedical Knowledge Graphs, including their component data sources.
Learn more about KG-Hub
- See the list of core graphs we maintain
- See the KG-Registry
- Browse all publicly available files stored on KG-Hub
- View the KG-Hub Dashboard
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.
KG-Hub also maintains:
- Tools for building your own KGs
- Code for building specific "core" KGs
- For example, KG-COVID-19
- The products of "core" KGs, in a convenient exchange format (KGX)
- A set of OBO ontologies as graph nodes and edges
- See KG-OBO
- A registry of our own and community-developed KGs and related data sources
- See KG-Registry
Design Principles
- Each core 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 KG-Hub can also provide a Docker image such that their code can be run easily as a container.
Core KG-Hub Projects
The table below lists core 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 |