Dear ResearchGate community,
I'm currently working with a large dataset of phytoplankton species, and I'm looking for a way to routinely update the taxonomy of these species. Specifically, I'm interested in identifying changes to scientific names, accepted names, synonyms, and higher-level taxonomic classifications.
I've tried using various R packages such as worrms to retrieve taxonomic information from online databases, but I've encountered some challenges with data quality and consistency.
I would appreciate any suggestions or advice on how to efficiently and accurately update the taxonomy of my dataset on a regular basis. Are there any reliable databases or APIs that I should be using, like AlgaeBase? Are there any best practices for handling taxonomic data in R?
Thank you for your help!
Nicolas
Maybe you can use taxonomy files from PR2? It is regularly updated and there is an R package: https://pr2database.github.io/pr2database/index.html
Hi Alex,
Thank you for your response. Unfortunately, I have found that "algaeClassify" no longer includes the "algae_search()" function for querying the Algaebase online taxonomic database in versions 1.3.0 and later (https://cran.r-project.org/web/packages/algaeClassify/index.html). I have tried to obtain an API key from Pier Kuipers, the lead developer of Algaebase, but I have not received a response yet.
Nicolas
Hi Nicolas,
Let me know if you get a response or any updates. I played around with it a while ago when it still was able to query Algaebasae to an extent.
I think the algaeClassify package has a lot of potential. However, Algaebase is still very much a work in progress with many synonyms (objective or subjective) of most species yet to be updated/included. At least common species are fairly complete...
Alex.
Hi Alex, I wanted to inform you that I finally received a response from AlgeaBase regarding the API key. I will be trying it out in the next couple of weeks and will get back to you with the results.
Hi Nicolas, I am dealing with updating the phytoplankton taxonomy and as you can see algae_search function is removed from algae_classify package. Do you have any idea about it please?
Hi Hana,
You have several ways to proceed. The first one is to use the worrms package (https://docs.ropensci.org/worrms/articles/worrms.html). This package can be a good alternative. The second one, which is a bit more complex, is to request an API key from the administrator of the Algaebase website (https://www.algaebase.org/api/). Afterwards, you will need to create a function in R that allows you to retrieve the information in JSON format and convert it into a dataframe. By the end of the year, I will post on my GitHub the functions that I have created/used to update my data.
Alternatively, you also have https://docs.ropensci.org/taxize/index.html. You can find a lot of information on this website as well: https://www.marinedatascience.co/data/.
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