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: 62 nodes and 37 edges
#> #
#> # A rooted forest with 25 trees
#> #
#> # Node Data: 62 × 17 (active)
#>    id         category pcategory name  symbol in_taxon_label description synonym
#>    <chr>      <list>   <chr>     <chr> <chr>  <chr>          <chr>       <list> 
#>  1 GO:0045892 <chr>    biolink:… nega… NA     NA             Any proces… <chr>  
#>  2 HGNC:8550  <chr>    biolink:… PA2G4 PA2G4  Homo sapiens   NA          <chr>  
#>  3 HGNC:10414 <chr>    biolink:… RPS26 RPS26  Homo sapiens   NA          <chr>  
#>  4 RGD:15829… <chr>    biolink:… Rps2… Rps26… Rattus norveg… NA          <chr>  
#>  5 GO:0015935 <chr>    biolink:… smal… NA     NA             The smalle… <chr>  
#>  6 GO:0019722 <chr>    biolink:… calc… NA     NA             Any intrac… <chr>  
#>  7 HGNC:4383  <chr>    biolink:… GNA15 GNA15  Homo sapiens   NA          <chr>  
#>  8 MONDO:010… <chr>    biolink:… over… NA     NA             A disease … <chr>  
#>  9 CLINVAR:1… <chr>    biolink:… NM_0… NA     Homo sapiens   NA          <lgl>  
#> 10 ZFA:00000… <chr>    biolink:… phar… NA     NA             Skeletal a… <chr>  
#> # ℹ 52 more rows
#> # ℹ 9 more variables: iri <chr>, namespace <chr>, provided_by <list>,
#> #   full_name <chr>, xref <list>, in_taxon <list>, type <list>,
#> #   has_gene <list>, deprecated <chr>
#> #
#> # Edge Data: 37 × 23
#>    from    to subject    predicate object primary_knowledge_so…¹ knowledge_level
#>   <int> <int> <chr>      <chr>     <chr>  <chr>                  <chr>          
#> 1     2     1 HGNC:8550  biolink:… GO:00… infores:mgi            knowledge_asse…
#> 2     3     4 HGNC:10414 biolink:… RGD:1… infores:panther        knowledge_asse…
#> 3     3     5 HGNC:10414 biolink:… GO:00… infores:uniprot        knowledge_asse…
#> # ℹ 34 more rows
#> # ℹ abbreviated name: ¹​primary_knowledge_source
#> # ℹ 16 more variables: negated <lgl>, original_subject <chr>,
#> #   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>,
#> #   qualifiers <list>, original_predicate <chr>, …