Overview

The Monarch Initiative is more than just this website, it is a whole ecosystem of related tools. This diagram illustrates the architecture of how it all fits together.

The three primary data types in the Monarch KG are genes, diseases, and phenotypes. The image below details their entity (node) and link (edge) counts and the unifying ontologies by which the source data and ontologies are harmonized. Cross-species inference is accomplished via gene orthology, homology, and phenotype similarity. Content dissemination is via API, the Monarch UI, and within the clinical application Exomiser. Note that the figure expresses only a portion of the integrated ontologies in column C. For a comprehensive list see PHENIO documentation (linked below).

Diagram of Monarch infrastructure, described below.
Data harmonization within the Monarch KG. (A) Data types and counts. (B, C, D) Data sources, ontologies, and knowledge graphs. (E) Cross-species inference. (F) Content dissemination
(Column D acronyms) GO: Gene Ontology; BP: Biological Process; MF: Molecular Function; CC: Cellular Component

Documentation, licensing, and other information for each piece in the Monarch architecture can be found on GitHub, Google, and elsewhere:

Monarch Initiative on GitHubPhenio on GitHub