Given a 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.
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")
# prints a readable summary and returns a list of dataframes
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>, …
# prints a readable summary and returns a list of dataframes
g <- monarch_engine() |> example_graph()
#> Trying to connect to https://neo4j.monarchinitiative.org
#> Connected to https://neo4j.monarchinitiative.org
print(g)
#> # A tbl_graph: 68 nodes and 41 edges
#> #
#> # A directed acyclic simple graph with 30 components
#> #
#> # Node Data: 68 × 17 (active)
#> id category pcategory name symbol description synonym full_name in_taxon
#> <chr> <list> <chr> <chr> <chr> <chr> <named> <chr> <named >
#> 1 NCBIG… <chr> biolink:… ATP5… ATP5F… ATP syntha… <lgl> ATP synt… <chr>
#> 2 GO:19… <chr> biolink:… prot… NA The direct… <chr> NA <lgl>
#> 3 dicty… <chr> biolink:… psmA3 psmA3 NA <lgl> psmA3 <chr>
#> 4 Xenba… <chr> biolink:… psma3 psma3 NA <chr> proteaso… <chr>
#> 5 GO:00… <chr> biolink:… spli… NA Any of a s… <chr> NA <lgl>
#> 6 NCBIG… <chr> biolink:… SNRN… SNRNP… small nucl… <lgl> small nu… <chr>
#> 7 GO:00… <chr> biolink:… posi… NA Any proces… <chr> NA <lgl>
#> 8 NCBIG… <chr> biolink:… TEK TEK TEK recept… <lgl> TEK rece… <chr>
#> 9 MONDO… <chr> biolink:… over… NA A disease … <chr> NA <lgl>
#> 10 CLINV… <chr> biolink:… NM_0… NA NA <lgl> NA <chr>
#> # ℹ 58 more rows
#> # ℹ 8 more variables: namespace <chr>, provided_by <named list>, iri <chr>,
#> # in_taxon_label <chr>, xref <named list>, type <named list>,
#> # has_gene <named list>, deprecated <chr>
#> #
#> # Edge Data: 41 × 22
#> from to subject predicate object knowledge_level negated
#> <int> <int> <chr> <chr> <chr> <chr> <lgl>
#> 1 1 2 NCBIGene:338081 biolink:act… GO:19… knowledge_asse… TRUE
#> 2 4 3 Xenbase:XB-GENE-976787 biolink:ort… dicty… knowledge_asse… NA
#> 3 6 5 NCBIGene:535113 biolink:par… GO:00… knowledge_asse… TRUE
#> # ℹ 38 more rows
#> # ℹ 15 more variables: primary_knowledge_source <chr>, original_subject <chr>,
#> # species_context_qualifier <chr>, agent_type <chr>, knowledge_source <chr>,
#> # aggregator_knowledge_source <named list>, has_evidence <named list>,
#> # provided_by <named list>, id <chr>, category <named list>,
#> # publications <named list>, qualifiers <named list>,
#> # original_predicate <chr>, disease_context_qualifier <chr>, …