rdf experiment

notebook/taxa-rdf.R

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+remotes::install_github("cboettig/virtuoso")
+remotes::install_github("cboettig/rdftools")
+
+library(virtuoso)
+library(readr)
+library(rdftools)
+library(dplyr)
+library(taxald)
+
+taxa_tbl("itis", "taxonid") %>%
+  collect() %>%
+  rdftools::write_nquads("itis_ids.nq.gz",
+                         key_column = "id",
+                         prefix = "taxald:")
+
+taxa_tbl("ncbi", "taxonid") %>% collect() %>%
+  rdftools::write_nquads("ncbi_ids.nq.gz",
+                         key_column = "id",
+                         prefix = "taxald:")
+taxa_tbl("col", "taxonid") %>% collect() %>%
+  rdftools::write_nquads("col_ids.nq.gz",
+                         key_column = "id",
+                         prefix = "taxald:")
+taxa_tbl("gbif", "taxonid") %>% collect() %>%
+  rdftools::write_nquads("gbif_ids.nq.gz",
+                         key_column = "id",
+                         prefix = "taxald:")
+taxa_tbl("tpl", "taxonid") %>% collect() %>%
+  rdftools::write_nquads("tpl_ids.nq.gz",
+                         key_column = "id",
+                         prefix = "taxald:")
+taxa_tbl("fb", "taxonid") %>% collect() %>%
+  rdftools::write_nquads("fb_ids.nq.gz",
+                         key_column = "id",
+                         prefix = "taxald:")
+taxa_tbl("slb", "taxonid") %>% collect() %>%
+  rdftools::write_nquads("slb_ids.nq.gz",
+                         key_column = "id",
+                         prefix = "taxald:")
+taxa_tbl("wd", "taxonid") %>% collect() %>%
+  rdftools::write_nquads("wd_ids.nq.gz",
+                         key_column = "id",
+                         prefix = "taxald:")
+#virtuoso:::vos_delete_db()
+vos_start()
+con <- vos_connect()
+files <- fs::dir_ls(glob="*.nq.gz")
+vos_import(con, files)
+
+
+vos_query(con,
+"SELECT * FROM <rdflib>
+ WHERE {
+    ?s ?p ?q
+} LIMIT 200
+")
+
+
+vos_query(con,
+"SELECT ?id ?name ?rank
+ WHERE {
+    ?id <taxald:name> ?name .
+    ?id <taxald:rank> ?rank
+} LIMIT 20
+")
+
+vos_query(con,
+'SELECT ?id ?rank
+ WHERE {
+    ?id <taxald:name> "Homo sapiens" .
+    ?id <taxald:rank> ?rank
+} LIMIT 20
+')
+
+vos_query(con,
+          'SELECT ?id ?name
+ WHERE {
+    ?id <taxald:name> ?name .
+    ?id <taxald:rank> "kingdom"
+} LIMIT 20
+')
+