Description of need: At present, the DWCA taxonomy download is a taxon list without synonymies. In order to work with iNaturalist data, and in particular to deal with both iNaturalist data and other data using other taxonomies, the full iNaturalist taxonomy including synonymies would be much more useful. At present it’s difficult to get that information by other means—see recent discussion here.
Feature request details: Changing the DWCA taxonomy download—or providing an additional download and leaving that one unchanged, I suppose—that corresponds to an “active=any” rather than “active=true” query and includes the “synonym_id” field would resolve the issue.
An update: as of submitting the feature request, I had figured out how to download the iNaturalist taxonomy, but I hadn’t yet done so. If others are curious, the “how” follows.
To get all the “inactive” names, use this helpful tool created by @pisum: https://jumear.github.io/stirfry/iNatAPIv1_taxa.html?taxon_id=47604&is_active=false. On iNaturalist, navigate to the higher-level taxon whose taxonomy you want to download, e.g.: https://www.inaturalist.org/taxa/47604-Asteraceae. Copy and paste the taxon_id into the URL above. If there are more than 10,000 results, you won’t be able to download them all. Open the iNaturalist pages for all taxa at the next rank down that are included within that taxon. Copy & paste taxon_ids for each of these, and continue moving down the taxonomic hierarchy as needed.
To download the iNaturalist taxonomy for land plants took me a total of 65 iterations of the copy / paste taxon_id & export csv process. Having done it… I think I’d rather not do it again.
this is more what i was thinking when i talked about “a handful of logical groupings” in the earlier post. sorry i didn’t provide more detail, since that may have saved on some extra work.
It could also be done more efficiently by me typing the tags correctly… accidentally writing “active” rather than “is_active” means I was actually just downloading the same data as in the DWCA file. Ho hum. Doing it correctly I end up with 65 downloads.
Also, for what it’s worth, that URL was merely illustrative—there isn’t a single iNaturalist taxon that corresponds with “land plants” a.k.a. Embryophyta, rather it would be at the highest level this set:
I am working through a database. The selection is lichenized and lichenophilic fungi. This is a scattered group in the Fungi kingdom. The SQL script allows me to get rid of the taxon ID search, tracking of the number of returned results.
So, yes. Importing synonyms into the taxonomic tree is a good idea.
Probably a dumb question, but how would one connect the inactive synonyms with the active taxon? Typically there is an active taxon field or something similar with lists of synonyms, that can be used to link the two.
These tables are very useful, but they don’t contain:
sysonyms for latin (scientific) names as in the title of this thread
information about which vernacular name (for example English) is main one. Because first name listed in the datasheet not always is main name. For examle in case of Caloptilia stigmatella:
“willow leafcone caterpillar” is listed as first one in the “VernacularNames-english.csv” file extracted from the “inaturalist-taxonomy.dwca.zip” archive, but
regarding @aspidoscelis main request of synonymy capture properly in the export itself,
I think the easiest way is to use is_valid on scientific names itself, for example, on this taxon page - https://www.inaturalist.org/taxa/946464-Eupterote-axesta, the synonym acesta is linked with original axesta, but its is_valid is false.
so I can think of correct way to do this cleanly for DWC maybe is:
we export junior synonym acesta as true single taxon in export, but link it to acceptedNameUsageID by linking to senior name axesta by finding such is_valid false scientific names during export itself; and also setting its taxonomicStatus to synonym instead of accepted for acesta