R/example_graph.file_engine.R
example_graph.file_engine.RdGiven a KGX file-based KG engine, returns a graph representing the diversity of node categories and edge predicates for browsing. The returned graph is guaranteed to contain at least one node of every category, and at least one edge of every predicate. No other guarantees are made: the example graph is not minimal to satisfy these criteria, it is not random or even pseudo-random, and it may not be connected.
# S3 method for class 'file_engine'
example_graph(engine, ...)A tbl_kgx graph
# Using example KGX file packaged with monarchr
filename <- system.file("extdata", "eds_marfan_kg.tar.gz", package = "monarchr")
# Retrieve and print an example graph:
g <- file_engine(filename) |> example_graph()
print(g)
#> # A tbl_graph: 12 nodes and 10 edges
#> #
#> # A directed acyclic multigraph with 3 components
#> #
#> # Node Data: 12 × 16 (active)
#> id pcategory name symbol in_taxon_label description synonym category
#> <chr> <chr> <chr> <chr> <chr> <chr> <list> <list>
#> 1 MONDO:000… biolink:… Marf… NA NA A disorder… <chr> <chr>
#> 2 MONDO:002… biolink:… Ehle… NA NA The Ehlers… <chr> <chr>
#> 3 MONDO:000… biolink:… Ehle… NA NA Ehlers-Dan… <chr> <chr>
#> 4 MONDO:001… biolink:… Ehle… NA NA A form of … <chr> <chr>
#> 5 ZFIN:ZDB-… biolink:… b3ga… NA Danio rerio NA <chr> <chr>
#> 6 HGNC:3603 biolink:… FBN1 FBN1 Homo sapiens NA <chr> <chr>
#> 7 HP:0000974 biolink:… Hype… NA NA A conditio… <chr> <chr>
#> 8 HP:0000007 biolink:… Auto… NA NA A mode of … <chr> <chr>
#> 9 MONDO:002… biolink:… rare NA NA A disease … <chr> <chr>
#> 10 CHEBI:508… biolink:… doxy… NA NA Tetracycli… <chr> <chr>
#> 11 CLINVAR:2… biolink:… NM_0… NA Homo sapiens NA <chr> <chr>
#> 12 CLINVAR:2… biolink:… NM_0… NA Homo sapiens NA <chr> <chr>
#> # ℹ 8 more variables: iri <chr>, xref <list>, namespace <chr>,
#> # provided_by <chr>, in_taxon <chr>, full_name <chr>, type <list>,
#> # has_gene <chr>
#> #
#> # Edge Data: 10 × 25
#> from to subject predicate object agent_type knowledge_level
#> <int> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 11 1 CLINVAR:200198 biolink:associat… MONDO… manual_ag… knowledge_asse…
#> 2 6 1 HGNC:3603 biolink:causes MONDO… manual_ag… knowledge_asse…
#> 3 6 1 HGNC:3603 biolink:gene_ass… MONDO… manual_ag… knowledge_asse…
#> # ℹ 7 more rows
#> # ℹ 18 more variables: knowledge_source <chr>,
#> # aggregator_knowledge_source <chr>, primary_knowledge_source <chr>,
#> # provided_by <chr>, id <chr>, category <chr>, original_object <chr>,
#> # original_subject <chr>, frequency_qualifier <chr>, has_evidence <chr>,
#> # has_total <dbl>, has_quotient <dbl>, has_count <dbl>, has_percentage <dbl>,
#> # onset_qualifier <chr>, publications <chr>, qualifiers <chr>, …