OTT id 5784010 could not be found

[LunaSare]

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.

[fmichonneau]

Sorry for the late reply @LunaSare! I think you are correct about this. There might be a way around it. I'd suggest you contact the OpenTree team to see if they can help further by submitting an issue at https://github.com/opentreeoflife/feedback.

[josephwb]

I missed this one too... @LunaSare I believe you are correct: I do not think there is a mechanism to update previously mapped names (or unmap deprecated names) when OTT is itself updated. You can browse OTT here.