Example Ehlers-Danlos and Marfan Syndrome Knowledge Graph Engine

Source: R/data_example_kgs.R

A small file_engine() Knowledge Graph (KG) containing Monarch Initiative data for Ehlers-Danlos Syndrome and Marfan Syndrome, including their subtypes, all entities connected to those diseases or subtypes, and all ancestors (supertypes) of all those diseases and entities. Generated 8/15/2024 via:

data(eds_marfan_kg)

Format

An object of class file_engine for use with fetch_nodes(), expand(), etc.

Details

monarch_engine() |>
    fetch_nodes(query_ids = c("MONDO:0020066", "MONDO:0007947")) |>
    expand(predicates = "biolink:subclass_of", direction = "in", transitive = TRUE) |>
    expand() |>
    expand(predicates = "biolink:subclass_of", direction = "out", transitive = TRUE)

This example engine may also be loaded from file via

filename <- system.file("extdata", "eds_marfan_kg.tar.gz", package = "monarchr")
eds_marfan_kg <- file_engine(filename)

Examples

data(eds_marfan_kg)
phenos <- eds_marfan_kg |>
          fetch_nodes(query_ids = "MONDO:0007525") |>
          expand(predicates = "biolink:has_phenotype",
                 categories = "biolink:PhenotypicFeature")