search

ropensci / taxize

A taxonomic toolbelt for R
https://docs.ropensci.org/taxize
Other
266 stars 59 forks source link

taxonomic databases update #826

Closed pecard closed 4 years ago

pecard commented 4 years ago

The taxonomic databases seem to be provided by globalnames.org. Some of the reference tables are not up to date. Is it something that can be easily adjusted or added manually?

sckott commented 4 years ago

The only data provided by global names is through the functions prefixed with gnr or gni, see https://github.com/ropensci/taxize#currently-implemented-in-taxize for a summary of data sources and functions they map to.

I don't run global names, so I can't update any data. @dimus would be the one to talk to - Dmitry, is there info somewhere on when data sources are/will be updated?

dimus commented 4 years ago

@sckott I am going to finish updating data sources next week (hopefully). It depends on CoL now. CoL team is planning to release a new version next week. After that major datasets will be updated. @pecard, I did not update some datasets for a while either because they are too small and nobody asked for their update, or because I only had access to them once, and lost it now. What are you looking for?

sckott commented 4 years ago

thanks @dimus !

pecard commented 4 years ago

looking for harmonizing data for vertebrates. I'm not being able to find a workflow to deal with data from different sources. I have data from eBird, gbif, different national (PT) atlas and a single reference list for vertebrates. There are several reference lists on taxize seems to be outdated (IUCN, eBird, Reptile DataBase).

sckott commented 4 years ago

@dimus Did you update datasets yet?

dimus commented 4 years ago

@sckott yes, both resolver.globalnames.org and index.globanames.org are updated 3 days ago

dimus commented 4 years ago

the following datasets are updated

2020 May-June [x] 1 CoL (once a year)

[x] 3 ITIS

[x] 4 NCBI

[x] 9 WoRMS

[x] 11 GBIF

[x] 12 EOL

[x] 167 IPNI

[x] 172 PaleoBioDB

[x] 179 OpenTreeTaxonomy (3.2)

[x] 181 IRMNG (once a year)

[x] 184 ASM Mammal Diversity Database

[x] 185 IOC World Bird List v10.1 is current

[x] 186 MCZbase

[x] 187 eBird/Clements

[x] 188 American Ornithological Society

[x] 189 Howard and Moore Complete Checklist of the Birds of the World

[x] 193 Myriatrix

sckott commented 4 years ago

awesome, thanks @dimus

sckott commented 4 years ago

@pecard databases updated, closing for now as this is not a taxize issue