Table 1.
KG-Hub projects.a
| Project name | Description | Size (nodes/edges), in thousands | Code repository URL |
|---|---|---|---|
| KG-COVID-19 | Knowledge concerning SARS-CoV-2, SARS-CoV, and MERS-CoV, including viral interactions with human proteins (Reese et al. 2021). Sourced from 10 different data sources and 4 OBO ontologies, this KG was incorporated into the N3C Enclave (Bennett et al. 2021), was used in the NVBL (https://science.osti.gov/nvbl) project to provide integrated publicly available data relevant to COVID-19, and has been used to identify drugs that may affect COVID-19 outcome (Chan et al. 2022, Reese et al. 2022). | 574/24 145 | https://github.com/Knowledge-Graph-Hub/kg-covid-19 |
| KG-Microbe | Data about microbial traits, environment types, carbon substrates, and taxonomy. Its contents unite bacterial and archeal phenotypes across a broad range of species, supporting identification of common metabolic and environmental patterns. | 276/535 | https://github.com/Knowledge-Graph-Hub/kg-microbe |
| KG-IDG | A graph assembled to support the Illuminating the Druggable Genome (IDG) project (https://druggablegenome.net/), with the objective of characterizing poorly-understood members of protein families that are frequently targeted by approved drugs. KG-IDG unifies structured data from 14 different sources concerning drugs, proteins, and diseases. | 560/4431 | https://github.com/Knowledge-Graph-Hub/kg-idg. |
| KG-OBO | A collection of OBO Foundry (https://obofoundry.org/) ontologies transformed into obograph JSON and graph-compatible KGX formats. 201 ontologies are currently included, many with multiple versions. | N/A | https://github.com/Knowledge-Graph-Hub/kg-obo. |
| ecoKG | Plant genes and traits, spanning 46 different species, with the objective of exploring gene, phenotype, and environment interactions. | 400/5000 | https://github.com/Knowledge-Graph-Hub/eco-kg. |
| KG-Monarch | A project to integrate data relevant to human diseases, especially rare diseases (Shefchek et al. 2020) (https://monarchinitiative.org). This includes 12 biomedical ontologies such as HPO, Mondo, and GO, data regarding human genes, diseases, phenotypes versus gene expression associations, as well as a range of data from many model organism databases. | 794/6970 | https://github.com/monarch-initiative/monarch-ingest |
| KG-Phenio | A KG representation of the Phenomics Integrated Ontology (PHENIO) (https://github.com/monarch-initiative/phenio), a resource combining more than 20 ontologies relevant to phenotype-driven biomedical research. | 275/1183 | https://github.com/Knowledge-Graph-Hub/kg-phenio |
a
For each of the seven KG-Hub projects, a description, size, and link to the project source code is provided.