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OTT id 5784010 could not be found
I obtained ott ids from the tip labels of a set of trees downloaded with rotl::get_study_tree
using the option tip_label = "ott_id"
When running:
tree <- rotl::get_study_tree(study_id="ot_1003", tree_id= "Tr100305", tip_label="ott_id")
ids <- tree$tip.label[!grepl("not_mapped", tree$tip.label)] # to remove unmapped taxa
ids <- unique(gsub("_.*", "", ids)) # to remove duplicated ott ids
taxon_info <- rotl::taxonomy_taxon_info(ids)
I get the error
Error: HTTP failure: 400
The OTT id 5784010 could not be foundBadInputExceptionorg.neo4j.server.rest.repr.BadInputExceptionlist("org.opentree.taxonomy.plugins.taxonomy_v3.taxon_info(taxonomy_v3.java:219)", "java.lang.reflect.Method.invoke(Method.java:498)", "org.neo4j.server.plugins.PluginMethod.invoke(PluginMethod.java:57)", "org.neo4j.server.plugins.PluginManager.invoke(PluginManager.java:168)", "org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:300)", "org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:122)", "java.lang.reflect.Method.invoke(Method.java:498)",
"org.neo4j.server.rest.security.SecurityFilter.doFilter(SecurityFilter.java:112)")
Inspecting the tree with names, that ott id was assigned to Solanum uncinellum, but that taxon does not appear anymore on the web page or looking for it with tnrs_match_names:
tree2 <- rotl::get_study_tree(study_id="ot_1003", tree_id= "Tr100305", tip_label="ott_taxon_name")
tree2$tip.label[grep("5784010", tree$tip.label)]
[1] "Solanum_uncinellum"
tnrs_match_names("Solanum uncinellum")
search_string unique_name approximate_match ott_id
1 solanum uncinellum Solanum uncinatum TRUE 6092431
is_synonym flags number_matches
1 FALSE SIBLING_HIGHER 2
Could this mean that tip names in already stored trees are not being updated with changes in OTT taxonomy?
Thanks.