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, ...)

Arguments

engine

A KG engine object

...

Other parameters (not used)

Value

A tbl_kgx graph

Examples

# 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 primary_knowledge_so…¹ agent_type
#>   <int> <int> <chr>          <chr>      <chr>  <chr>                  <chr>     
#> 1    11     1 CLINVAR:200198 biolink:a… MONDO… infores:clingen        manual_ag…
#> 2     6     1 HGNC:3603      biolink:c… MONDO… infores:omim           manual_ag…
#> 3     6     1 HGNC:3603      biolink:g… MONDO… infores:orphanet       manual_ag…
#> # ℹ 7 more rows
#> # ℹ abbreviated name: ¹​primary_knowledge_source
#> # ℹ 18 more variables: knowledge_level <chr>, knowledge_source <chr>,
#> #   aggregator_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>, …

# 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: 63 nodes and 37 edges
#> #
#> # A directed acyclic multigraph with 27 components
#> #
#> # Node Data: 63 × 16 (active)
#>    id         category pcategory name  symbol in_taxon_label description synonym
#>    <chr>      <list>   <chr>     <chr> <chr>  <chr>          <chr>       <list> 
#>  1 GO:0006493 <chr>    biolink:… prot… NA     NA             A protein … <chr>  
#>  2 RGD:62060  <chr>    biolink:… Ogt   Ogt    Rattus norveg… NA          <chr>  
#>  3 NCBIGene:… <chr>    biolink:… OGT   OGT    Canis lupus f… O-linked N… <lgl>  
#>  4 GO:0000123 <chr>    biolink:… hist… NA     NA             A protein … <chr>  
#>  5 RGD:3982   <chr>    biolink:… Yy1   Yy1    Rattus norveg… NA          <chr>  
#>  6 GO:0010467 <chr>    biolink:… gene… NA     NA             The proces… <lgl>  
#>  7 MONDO:010… <chr>    biolink:… over… NA     NA             A disease … <chr>  
#>  8 CLINVAR:1… <chr>    biolink:… NM_0… NA     Homo sapiens   NA          <lgl>  
#>  9 OBA:20500… <chr>    biolink:… seru… NA     NA             The amount… <chr>  
#> 10 HP:0003542 <chr>    biolink:… Incr… NA     NA             The concen… <chr>  
#> # ℹ 53 more rows
#> # ℹ 8 more variables: iri <chr>, xref <list>, namespace <chr>,
#> #   provided_by <list>, full_name <chr>, in_taxon <list>, type <list>,
#> #   has_gene <list>
#> #
#> # Edge Data: 37 × 22
#>    from    to subject   predicate  object primary_knowledge_so…¹ knowledge_level
#>   <int> <int> <chr>     <chr>      <chr>  <chr>                  <chr>          
#> 1     2     1 RGD:62060 biolink:a… GO:00… infores:rgd            knowledge_asse…
#> 2     2     3 RGD:62060 biolink:o… NCBIG… infores:panther        knowledge_asse…
#> 3     2     4 RGD:62060 biolink:p… GO:00… infores:rgd            knowledge_asse…
#> # ℹ 34 more rows
#> # ℹ abbreviated name: ¹​primary_knowledge_source
#> # ℹ 15 more variables: negated <lgl>, species_context_qualifier <chr>,
#> #   agent_type <chr>, knowledge_source <chr>,
#> #   aggregator_knowledge_source <list>, has_evidence <list>,
#> #   provided_by <list>, id <chr>, category <list>, publications <list>,
#> #   original_object <chr>, qualifiers <list>, original_predicate <chr>, …