maxo's Journal

12 de abril de 2023

CNPS Rare Plants on iNaturalist

I imported the entire Rare Plants database into a set of iNaturalist Projects. CNPS Rare Plants (https://rareplants.cnps.org/) is an inventory of over 2400 plants and their various rarity rankings throughout the CFP (California Floristic Province). Lots of land managers, policy makers, and activists use CNPS rare plant statuses to protect ecosystems across the state, so I wanted to make it easy to track them on iNat.

The umbrella project for all ranking levels is https://www.inaturalist.org/projects/cnps-rare-plants.

An example of what can be done with a project is something like this... all of the research grade rare plant IDs in the Eaton Canyon Biodiversity Area https://www.inaturalist.org/observations?place_id=162459&project_id=cnps-rare-plants&quality_grade=research&subview=map&verifiable=any

You'll notice the umbrella project has around 1700 species, but I mentioned 2400 above. All 2400+ have been added to the project, but only ~1700 have any observations, meaning there are ~700 rare plant species out there that haven't been put on iNaturalist in the CFP yet. The Rare Plants project is set up to only show observations with the CFP boundary, so observations in e.g. Oregon wouldn't show up here.

There are a few missing species due to differences in iNaturalist's taxonomy. Generally iNat gets taxonomy info from Kew Gardens POWO database. If CNPS disagrees with POWO, then there might not be a way to express a rare species, variety or subspecies on iNat. One example of this is the 1A plant Lycium verrucosum (San Nicolas Island desert-thorn) which is considered by POWO to be the more common Lycium brevipes. In these cases I just use the POWO synonym species, but in the case of San Nicolas Island desert-thorn, this means any Lycium brevipes observation will show up as a 1A rare plant, even though Lycium brevipes is not in the CNPS rare plant registry. iNaturalist's own 1A tag (which are not available as search parameters, hence the need for me to create this project) shows that Lycium brevipes is a 1A rare plant as well https://www.inaturalist.org/taxa/77903-Lycium-brevipes. Should I be handling this differently? Let me know.

The code used to create this project is here https://github.com/maxogden/inaturalist-taxonomy-import and the data is here https://docs.google.com/spreadsheets/d/1-c45X-BvIVbgSPacDXsyR9OIywnIWtghAa1_K3lS6v8/edit?usp=sharing. The general approach was to:

Download the iNaturalist DWCA Taxonomy database
Download the CNPS rare plant database
For each binomial name in the CNPS data, try finding an exact match in the iNat taxonomy data to find the corresponding iNat taxon ID
For ones where an exact match is not available, fall back to the iNaturalist taxonomy API endpoint (which handles renamed taxons and other edge cases but is slower)
For anything that was not assigned a taxon ID, manually go through and find the correct taxon ID
Finally, once everything has a taxon ID, reverse engineer the iNaturalist project API (not documented) and add the ~2400 species to the 8 different projects in an automated way (so I didn't have to type them one at a time)

If you have any suggestions or ideas, please comment below

Posted on 12 de abril de 2023, 02:26 AM by

maxo | 0 comentários | Deixar um comentário

03 de maio de 2023

California Native, Invasive, Endangered and Special species on iNaturalist

12 de abril de 2023

CNPS Rare Plants on iNaturalist

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