diff --git a/articles/examples/alzheimers_phenotypes.html b/articles/examples/alzheimers_phenotypes.html index 814d849..8d2d88d 100644 --- a/articles/examples/alzheimers_phenotypes.html +++ b/articles/examples/alzheimers_phenotypes.html @@ -99,7 +99,7 @@

Vignette updated: Dec-24-2024

- Source: vignettes/examples/alzheimers_phenotypes.Rmd + Source: vignettes/examples/alzheimers_phenotypes.Rmd diff --git a/articles/examples/alzheimers_phenotypes_files/figure-html/unnamed-chunk-15-1.png b/articles/examples/alzheimers_phenotypes_files/figure-html/unnamed-chunk-15-1.png index 5cf2d71..0fa582f 100644 Binary files a/articles/examples/alzheimers_phenotypes_files/figure-html/unnamed-chunk-15-1.png and b/articles/examples/alzheimers_phenotypes_files/figure-html/unnamed-chunk-15-1.png differ diff --git a/articles/examples/alzheimers_phenotypes_files/figure-html/unnamed-chunk-7-1.png b/articles/examples/alzheimers_phenotypes_files/figure-html/unnamed-chunk-7-1.png index 7573ddd..a7d3697 100644 Binary files a/articles/examples/alzheimers_phenotypes_files/figure-html/unnamed-chunk-7-1.png and b/articles/examples/alzheimers_phenotypes_files/figure-html/unnamed-chunk-7-1.png differ diff --git a/articles/examples/exploring_kgs.html b/articles/examples/exploring_kgs.html index 86b6af9..3086e56 100644 --- a/articles/examples/exploring_kgs.html +++ b/articles/examples/exploring_kgs.html @@ -99,7 +99,7 @@

Vignette updated: Dec-24-2024

- Source: vignettes/examples/exploring_kgs.Rmd + Source: vignettes/examples/exploring_kgs.Rmd diff --git a/articles/examples/visualizing_kgs.html b/articles/examples/visualizing_kgs.html index 73d939e..df0a6d6 100644 --- a/articles/examples/visualizing_kgs.html +++ b/articles/examples/visualizing_kgs.html @@ -98,7 +98,7 @@

Vignette updated: Dec-24-2024

- Source: vignettes/examples/visualizing_kgs.Rmd + Source: vignettes/examples/visualizing_kgs.Rmd diff --git a/articles/monarchr.html b/articles/monarchr.html index 8db0104..d599151 100644 --- a/articles/monarchr.html +++ b/articles/monarchr.html @@ -99,7 +99,7 @@

Vignette updated: Dec-24-2024

- Source: vignettes/monarchr.Rmd + Source: vignettes/monarchr.Rmd @@ -6412,6 +6412,42 @@

Semantic Similarity +“HP:0430043” + + +“biolink:PhenotypicFeature” + + +“Thoracic lordosis” + + +“Thoracic lordosis refers to an abnormal curvature of the thoracic spine +in which the thoracic spine displays lordosis (inward curve) instead of +the normal kyphosis (outward curve).” + + +NA + + +c(“biolink:BiologicalEntity”, “biolink:DiseaseOrPhenotypicFeature”, +“biolink:Entity”, “biolink:NamedThing”, “biolink:PhenotypicFeature”, +“biolink:ThingWithTaxon”) + + +“http://purl.obolibrary.org/obo/HP_0430043” + + +NA + + +“HP” + + +“phenio_nodes” + + + + “HP:0001377” @@ -6528,41 +6564,6 @@

Semantic Similarity -“HP:0025586” - - -“biolink:PhenotypicFeature” - - -“Hypertropia” - - -“A type of strabismus characterized by permanent upward deviation of the -visual axis of one eye.” - - -NA - - -c(“biolink:BiologicalEntity”, “biolink:DiseaseOrPhenotypicFeature”, -“biolink:Entity”, “biolink:NamedThing”, “biolink:PhenotypicFeature”, -“biolink:ThingWithTaxon”) - - -“http://purl.obolibrary.org/obo/HP_0025586” - - -NA - - -“HP” - - -“phenio_nodes” - - - - “HP:0000518” @@ -6648,7 +6649,7 @@

Semantic Similarity -“HP:0001377” +“HP:0430043” “ancestor_information_content” @@ -6665,7 +6666,7 @@

Semantic Similarity -16 +17 “HP:0000974” @@ -6674,7 +6675,7 @@

Semantic Similarity -“HP:0025586” +“HP:0000518” “ancestor_information_content” @@ -6691,7 +6692,7 @@

Semantic Similarity -14 +13 “HP:0001027” @@ -6700,7 +6701,7 @@

Semantic Similarity -“HP:0000486” +“HP:0430043” “ancestor_information_content” @@ -6717,7 +6718,7 @@

Semantic Similarity -16 +14 “HP:0001030” @@ -6726,7 +6727,7 @@

Semantic Similarity -“HP:0025586” +“HP:0001377” “ancestor_information_content” @@ -6743,7 +6744,7 @@

Semantic Similarity -17 +15 “HP:0001058” @@ -6752,7 +6753,7 @@

Semantic Similarity -“HP:0000518” +“HP:0000486” “ancestor_information_content” @@ -6769,7 +6770,7 @@

Semantic Similarity -15 +16 “HP:0001065” @@ -6795,7 +6796,7 @@

Semantic Similarity -15 +16 “HP:0001073” @@ -6821,7 +6822,7 @@

Semantic Similarity -15 +16 “HP:0001075” @@ -6847,7 +6848,7 @@

Semantic Similarity -15 +16 “HP:0001252” @@ -6873,7 +6874,7 @@

Semantic Similarity -13 +14 “HP:0002761” diff --git a/articles/monarchr_files/figure-html/unnamed-chunk-13-1.png b/articles/monarchr_files/figure-html/unnamed-chunk-13-1.png index 9a075db..5e1d130 100644 Binary files a/articles/monarchr_files/figure-html/unnamed-chunk-13-1.png and b/articles/monarchr_files/figure-html/unnamed-chunk-13-1.png differ diff --git a/articles/monarchr_files/figure-html/unnamed-chunk-14-1.png b/articles/monarchr_files/figure-html/unnamed-chunk-14-1.png index 6ad0c0b..d23b84f 100644 Binary files a/articles/monarchr_files/figure-html/unnamed-chunk-14-1.png and b/articles/monarchr_files/figure-html/unnamed-chunk-14-1.png differ diff --git a/authors.html b/authors.html index 858fc5b..dc8bb6a 100644 --- a/authors.html +++ b/authors.html @@ -81,7 +81,7 @@

Authors and Citation

diff --git a/news/index.html b/news/index.html index 4039bd4..ec36198 100644 --- a/news/index.html +++ b/news/index.html @@ -65,7 +65,7 @@

Changelog

- Source: NEWS.md + Source: NEWS.md
diff --git a/pkgdown.yml b/pkgdown.yml index d3a8fd6..c78116b 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -6,4 +6,4 @@ articles: examples/exploring_kgs: examples/exploring_kgs.html monarchr: monarchr.html examples/visualizing_kgs: examples/visualizing_kgs.html -last_built: 2024-12-24T18:33Z +last_built: 2024-12-24T19:05Z diff --git a/reference/base_engine.html b/reference/base_engine.html index 99bd216..577ef34 100644 --- a/reference/base_engine.html +++ b/reference/base_engine.html @@ -65,7 +65,7 @@

base_engine

- Source: R/base_engine.R + Source: R/base_engine.R
diff --git a/reference/cypher_query.html b/reference/cypher_query.html index 7d0b0dc..0853abf 100644 --- a/reference/cypher_query.html +++ b/reference/cypher_query.html @@ -65,7 +65,7 @@

Execute a Cypher Query

- Source: R/cypher_query.R + Source: R/cypher_query.R
diff --git a/reference/cypher_query_df.html b/reference/cypher_query_df.html index 637bfe9..c4bd647 100644 --- a/reference/cypher_query_df.html +++ b/reference/cypher_query_df.html @@ -65,7 +65,7 @@

Execute a Cypher Query

- Source: R/cypher_query_df.R + Source: R/cypher_query_df.R
diff --git a/reference/cytoscape.html b/reference/cytoscape.html index 21b4ae0..76ca04c 100644 --- a/reference/cytoscape.html +++ b/reference/cytoscape.html @@ -72,7 +72,7 @@

Send a graph to Cytoscape

- Source: R/cytoscape.R + Source: R/cytoscape.R
diff --git a/reference/cytoscape.tbl_kgx.html b/reference/cytoscape.tbl_kgx.html index 970d955..fdbe8ea 100644 --- a/reference/cytoscape.tbl_kgx.html +++ b/reference/cytoscape.tbl_kgx.html @@ -72,7 +72,7 @@

Send a graph to Cytoscape

- Source: R/cytoscape.tbl_kgx.R + Source: R/cytoscape.tbl_kgx.R
diff --git a/reference/edges.html b/reference/edges.html index b99c8b4..6b2a5ed 100644 --- a/reference/edges.html +++ b/reference/edges.html @@ -65,7 +65,7 @@

Get graph edges table.

- Source: R/utils.R + Source: R/utils.R
diff --git a/reference/example_graph.file_engine.html b/reference/example_graph.file_engine.html index 1f49c15..7d5d13d 100644 --- a/reference/example_graph.file_engine.html +++ b/reference/example_graph.file_engine.html @@ -70,7 +70,7 @@

Return an example set of nodes from a KG engine.

- Source: R/example_graph.file_engine.R + Source: R/example_graph.file_engine.R
diff --git a/reference/example_graph.html b/reference/example_graph.html index 3420cc1..a35ff54 100644 --- a/reference/example_graph.html +++ b/reference/example_graph.html @@ -70,7 +70,7 @@

Return an example set of nodes from a KG engine.

- Source: R/example_graph.R + Source: R/example_graph.R
diff --git a/reference/example_graph.neo4j_engine.html b/reference/example_graph.neo4j_engine.html index ac23605..a1cef8f 100644 --- a/reference/example_graph.neo4j_engine.html +++ b/reference/example_graph.neo4j_engine.html @@ -70,7 +70,7 @@

Return an example set of nodes from a KG engine.

- Source: R/example_graph.neo4j_engine.R + Source: R/example_graph.neo4j_engine.R
diff --git a/reference/expand.html b/reference/expand.html index 063b01a..b816522 100644 --- a/reference/expand.html +++ b/reference/expand.html @@ -68,7 +68,7 @@

Fetch additional knowledge graph edges connected to a query graph

- Source: R/expand.R + Source: R/expand.R
diff --git a/reference/explode.html b/reference/explode.html index dc9903c..3ed4f46 100644 --- a/reference/explode.html +++ b/reference/explode.html @@ -65,7 +65,7 @@

Explode a graph into a list of single-node graphs

- Source: R/utils.R + Source: R/utils.R
diff --git a/reference/fetch_nodes.html b/reference/fetch_nodes.html index b9c6b22..255e29b 100644 --- a/reference/fetch_nodes.html +++ b/reference/fetch_nodes.html @@ -69,7 +69,7 @@

Fetch nodes from a graph using a set of IDs or conditions

- Source: R/fetch_nodes.R + Source: R/fetch_nodes.R
diff --git a/reference/file_engine.html b/reference/file_engine.html index f0979fc..c4d692d 100644 --- a/reference/file_engine.html +++ b/reference/file_engine.html @@ -65,7 +65,7 @@

Create a knowledge graph engine object from a KGX-based tsv file

- Source: R/file_engine.R + Source: R/file_engine.R
diff --git a/reference/file_engine_check.html b/reference/file_engine_check.html index 2859b69..f7473b3 100644 --- a/reference/file_engine_check.html +++ b/reference/file_engine_check.html @@ -65,7 +65,7 @@

Check availability of a file-based engine

- Source: R/file_engine_check.R + Source: R/file_engine_check.R
diff --git a/reference/get_engine.html b/reference/get_engine.html index 4d9ffe9..747a310 100644 --- a/reference/get_engine.html +++ b/reference/get_engine.html @@ -65,7 +65,7 @@

Get most recent engine from a graph.

- Source: R/get_engine.R + Source: R/get_engine.R
diff --git a/reference/get_engine.tbl_kgx.html b/reference/get_engine.tbl_kgx.html index 1ddfe8a..0ebe44f 100644 --- a/reference/get_engine.tbl_kgx.html +++ b/reference/get_engine.tbl_kgx.html @@ -65,7 +65,7 @@

Get most recent engine from a graph.

- Source: R/get_engine.tbl_kgx.R + Source: R/get_engine.tbl_kgx.R
diff --git a/reference/grapes-in_list-grapes.html b/reference/grapes-in_list-grapes.html index 531d8a3..4b4bf25 100644 --- a/reference/grapes-in_list-grapes.html +++ b/reference/grapes-in_list-grapes.html @@ -66,7 +66,7 @@

Check if an element is contained in list sub-elements

- Source: R/in_list.R + Source: R/in_list.R
diff --git a/reference/grapes-twiddle-grapes.html b/reference/grapes-twiddle-grapes.html index 68ef2f6..1768bf0 100644 --- a/reference/grapes-twiddle-grapes.html +++ b/reference/grapes-twiddle-grapes.html @@ -65,7 +65,7 @@

Infix regular expression match.

- Source: R/regex_tilde.R + Source: R/regex_tilde.R
diff --git a/reference/kg_join.html b/reference/kg_join.html index b9bc1f8..8d84df9 100644 --- a/reference/kg_join.html +++ b/reference/kg_join.html @@ -67,7 +67,7 @@

Join two KGX graphs by their nodes and edges.

- Source: R/kg_join.R + Source: R/kg_join.R
diff --git a/reference/knit_print.tbl_kgx.html b/reference/knit_print.tbl_kgx.html index e69f160..a89a306 100644 --- a/reference/knit_print.tbl_kgx.html +++ b/reference/knit_print.tbl_kgx.html @@ -65,7 +65,7 @@

Specialized print function for KGX graphs in knitted documents

- Source: R/knit_print.tbl_kgx.R + Source: R/knit_print.tbl_kgx.R
diff --git a/reference/load_kgx.html b/reference/load_kgx.html index 2ceb325..43bb0e6 100644 --- a/reference/load_kgx.html +++ b/reference/load_kgx.html @@ -67,7 +67,7 @@

Load a graph from a KGX-formatted .tar.gz file.

- Source: R/load_kgx.R + Source: R/load_kgx.R
diff --git a/reference/monarch_engine.html b/reference/monarch_engine.html index ed77c38..5db9b29 100644 --- a/reference/monarch_engine.html +++ b/reference/monarch_engine.html @@ -66,7 +66,7 @@

Create a knowledge graph engine object backed by the public Monarch Neo4j instance

- Source: R/monarch_engine.R + Source: R/monarch_engine.R
diff --git a/reference/monarch_engine_check.html b/reference/monarch_engine_check.html index 4490031..73e78eb 100644 --- a/reference/monarch_engine_check.html +++ b/reference/monarch_engine_check.html @@ -65,7 +65,7 @@

Check availability of Monarch Initiative API

- Source: R/monarch_engine_check.R + Source: R/monarch_engine_check.R
diff --git a/reference/monarch_search.html b/reference/monarch_search.html index eb1a03a..b5ca43f 100644 --- a/reference/monarch_search.html +++ b/reference/monarch_search.html @@ -67,7 +67,7 @@

Search for KG nodes using the Monarch Initiative search API

- Source: R/monarch_search.R + Source: R/monarch_search.R
diff --git a/reference/monarch_semsim.html b/reference/monarch_semsim.html index e947b43..a994e26 100644 --- a/reference/monarch_semsim.html +++ b/reference/monarch_semsim.html @@ -67,7 +67,7 @@

Semantic similarity mapping between two graphs

- Source: R/monarch_semsim.R + Source: R/monarch_semsim.R
@@ -160,11 +160,11 @@

Examples

#> Joining with `by = join_by(id, pcategory, name, description, synonym, category, #> iri, xref, namespace, provided_by)` print(sim) -#> # A tbl_graph: 134 nodes and 107 edges +#> # A tbl_graph: 137 nodes and 107 edges #> # -#> # A directed multigraph with 39 components +#> # A directed multigraph with 42 components #> # -#> # Node Data: 134 × 10 (active) +#> # Node Data: 137 × 10 (active) #> id pcategory name description synonym category iri xref namespace #> <chr> <chr> <chr> <chr> <named> <list> <chr> <nam> <chr> #> 1 MONDO:000… biolink:… Marf… A disorder… <chr> <chr> http… <chr> MONDO @@ -177,15 +177,15 @@

Examples

#> 8 HP:0003199 biolink:… Decr… NA <chr> <chr> http… <chr> HP #> 9 HP:0025586 biolink:… Hype… A type of … <lgl> <chr> http… <lgl> HP #> 10 HP:0000518 biolink:… Cata… A cataract… <chr> <chr> http… <chr> HP -#> # ℹ 124 more rows +#> # ℹ 127 more rows #> # ℹ 1 more variable: provided_by <named list> #> # #> # Edge Data: 107 × 8 #> from to subject predicate object metric score ancestor_id #> <int> <int> <chr> <chr> <chr> <chr> <dbl> <chr> -#> 1 107 126 HP:0000006 computed:best_matches HP:0003… ances… 4.33 HP:0000001 +#> 1 107 126 HP:0000006 computed:best_matches HP:0002… ances… 4.33 HP:0000001 #> 2 84 84 HP:0000023 computed:best_matches HP:0000… ances… 18.5 HP:0000023 -#> 3 24 115 HP:0000098 computed:best_matches HP:0000… ances… 6.25 UPHENO:000… +#> 3 24 117 HP:0000098 computed:best_matches HP:0000… ances… 6.25 UPHENO:000… #> # ℹ 104 more rows # also inclue the unmatched targets @@ -218,7 +218,7 @@

Examples

#> # Edge Data: 107 × 8 #> from to subject predicate object metric score ancestor_id #> <int> <int> <chr> <chr> <chr> <chr> <dbl> <chr> -#> 1 107 115 HP:0000006 computed:best_matches HP:0001… ances… 4.33 HP:0000001 +#> 1 107 144 HP:0000006 computed:best_matches HP:0003… ances… 4.33 HP:0000001 #> 2 84 84 HP:0000023 computed:best_matches HP:0000… ances… 18.5 HP:0000023 #> 3 24 126 HP:0000098 computed:best_matches HP:0000… ances… 6.25 UPHENO:000… #> # ℹ 104 more rows @@ -232,7 +232,7 @@

Examples

print(sim) #> # A tbl_graph: 162 nodes and 174 edges #> # -#> # A directed multigraph with 29 components +#> # A directed multigraph with 28 components #> # #> # Node Data: 162 × 10 (active) #> id pcategory name description synonym category iri xref namespace @@ -253,7 +253,7 @@

Examples

#> # Edge Data: 174 × 8 #> from to subject predicate object metric score ancestor_id #> <int> <int> <chr> <chr> <chr> <chr> <dbl> <chr> -#> 1 107 40 HP:0000006 computed:best_matches HP:0001… ances… 4.33 HP:0000001 +#> 1 107 158 HP:0000006 computed:best_matches HP:0030… ances… 4.33 HP:0000001 #> 2 84 84 HP:0000023 computed:best_matches HP:0000… ances… 18.5 HP:0000023 #> 3 24 126 HP:0000098 computed:best_matches HP:0000… ances… 6.25 UPHENO:000… #> # ℹ 171 more rows diff --git a/reference/neo2r_to_kgx.html b/reference/neo2r_to_kgx.html index f967914..2b5970b 100644 --- a/reference/neo2r_to_kgx.html +++ b/reference/neo2r_to_kgx.html @@ -66,7 +66,7 @@

Process neo2R cypher to tbl_kgx

- Source: R/cypher_query.neo4j_engine.R + Source: R/cypher_query.neo4j_engine.R
diff --git a/reference/neo4j_engine.html b/reference/neo4j_engine.html index 1c88501..6f3b90d 100644 --- a/reference/neo4j_engine.html +++ b/reference/neo4j_engine.html @@ -67,7 +67,7 @@

Create a knowledge graph engine object for a neo4j database

- Source: R/neo4j_engine.R + Source: R/neo4j_engine.R
diff --git a/reference/neo4j_engine_check.html b/reference/neo4j_engine_check.html index b97fa44..7e90f30 100644 --- a/reference/neo4j_engine_check.html +++ b/reference/neo4j_engine_check.html @@ -65,7 +65,7 @@

Check if a neo4j database is available and properly formatted

- Source: R/neo4j_engine_check.R + Source: R/neo4j_engine_check.R
diff --git a/reference/nodes.html b/reference/nodes.html index 261fc06..6023b0b 100644 --- a/reference/nodes.html +++ b/reference/nodes.html @@ -65,7 +65,7 @@

Get graph nodes table.

- Source: R/utils.R + Source: R/utils.R
diff --git a/reference/normalize_categories.html b/reference/normalize_categories.html index 119272d..6093a20 100644 --- a/reference/normalize_categories.html +++ b/reference/normalize_categories.html @@ -66,7 +66,7 @@

Normalize Categories

- Source: R/normalize_categories.R + Source: R/normalize_categories.R
diff --git a/reference/order_cols.html b/reference/order_cols.html index 1c64658..f2aeba0 100644 --- a/reference/order_cols.html +++ b/reference/order_cols.html @@ -65,7 +65,7 @@

Set edge/row data column order according to most recent engine preferences

- Source: R/order_cols.R + Source: R/order_cols.R
diff --git a/reference/plot.tbl_kgx.html b/reference/plot.tbl_kgx.html index 7fd67d7..f1e3779 100644 --- a/reference/plot.tbl_kgx.html +++ b/reference/plot.tbl_kgx.html @@ -65,7 +65,7 @@

Specialized plot() function for KGX graphs

- Source: R/plot.tbl_kgx.R + Source: R/plot.tbl_kgx.R
diff --git a/reference/save_kgx.html b/reference/save_kgx.html index 2b66b5d..dadb777 100644 --- a/reference/save_kgx.html +++ b/reference/save_kgx.html @@ -68,7 +68,7 @@

Save a graph as a KGX-formatted .tar.gz file.

- Source: R/save_kgx.R + Source: R/save_kgx.R
diff --git a/reference/set_engine.html b/reference/set_engine.html index d64dcb8..d402efa 100644 --- a/reference/set_engine.html +++ b/reference/set_engine.html @@ -70,7 +70,7 @@

Set the engine for a graph. See warning in details.

- Source: R/set_engine.R, R/set_engine.tbl_kgx.R + Source: R/set_engine.R, R/set_engine.tbl_kgx.R
diff --git a/reference/stitch_vectors.html b/reference/stitch_vectors.html index a954c0d..b4046f6 100644 --- a/reference/stitch_vectors.html +++ b/reference/stitch_vectors.html @@ -68,7 +68,7 @@

Stitch Vectors

- Source: R/cypher_query.neo4j_engine.R + Source: R/cypher_query.neo4j_engine.R
diff --git a/reference/summarize_neighborhood.html b/reference/summarize_neighborhood.html index 34826b0..2c563b0 100644 --- a/reference/summarize_neighborhood.html +++ b/reference/summarize_neighborhood.html @@ -69,7 +69,7 @@

Summarize neighborhood

- Source: R/summarize_neighborhood.R + Source: R/summarize_neighborhood.R
diff --git a/reference/summary.file_engine.html b/reference/summary.file_engine.html index f9523b9..bae9755 100644 --- a/reference/summary.file_engine.html +++ b/reference/summary.file_engine.html @@ -70,7 +70,7 @@

Summarize contents of a KGX-file-based KG engine

- Source: R/summary.file_engine.R + Source: R/summary.file_engine.R
diff --git a/reference/summary.neo4j_engine.html b/reference/summary.neo4j_engine.html index 28cd09f..69c2e1c 100644 --- a/reference/summary.neo4j_engine.html +++ b/reference/summary.neo4j_engine.html @@ -70,7 +70,7 @@

Summarize contents of a Neo4j KG engine

- Source: R/summary.neo4j_engine.R + Source: R/summary.neo4j_engine.R
diff --git a/reference/tbl_kgx.html b/reference/tbl_kgx.html index fc516c7..d81f5b5 100644 --- a/reference/tbl_kgx.html +++ b/reference/tbl_kgx.html @@ -69,7 +69,7 @@

Create a KGX graph object

- Source: R/tbl_kgx.R + Source: R/tbl_kgx.R