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I am looking for a taxonomic dataset that would allow me to links tree genera (or species) to families. In particular, I am interested in the tropical species found in the Amazon.

I found a long but not exhaustive list on Wikipedia: https://en.wikipedia.org/wiki/List_of_trees_and_shrubs_by_taxonomic_family

After processing it, I realised it contains information about 404 genera, while the dataset I am dealing with has around 600. (in the end, I only got 23% of my data covered, very sad)

Does anyone know if such a crosswalk file exists, in some scientific article or somewhere in the Internet?

Moreover, please tell me if there are other StackExchange websites which could be more appropriate, I wasn't sure of where to post this.

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  • $\begingroup$ Contact Kew. BTW when emailing them make sure you call them genera. $\endgroup$ – Michael G. Jul 18 at 23:10
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    $\begingroup$ Thanks, it is always good to learn something new! $\endgroup$ – Davide Jul 22 at 15:17
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Probably the best currently available online database is RBG Kew's Plants of the World Online. It organises taxonomic, morphological and distribution data from a range of databases. You can search for your taxa of interest and find their associated higher ranks.

Alternatively, there is World Flora Online, replacing the now-defunct The Plant List v1.1, which also integrates taxonomic data from a range of reliable sources and national lists.

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  • $\begingroup$ Thanks! RBG Kew's site looks great, do you know if I can somehow download the data? $\endgroup$ – Davide Jul 19 at 20:14
  • $\begingroup$ Hi @Davide - you should use the dedicated APIs: either pykew for python, or taxize for R. $\endgroup$ – NatWH Jul 20 at 9:47
  • $\begingroup$ Thanks @NatWH, I'll look pykew up $\endgroup$ – Davide Jul 22 at 15:18
  • $\begingroup$ Hey @NatWH, I am having problems with using pykew, and I cannot find many usage examples. To do what I am asking I try to use the function powo.search({Name.genus = 'Poa'}), for example, and I just get the answer <pykew.core.SearchResult object at 0x00000231EBA12DA0>, and I don`t know how to extract the family name out of it... $\endgroup$ – Davide Jul 23 at 15:05
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    $\begingroup$ Actually realised that my data is not perfect: the correct spelling of that genus is 'Ziziphus' - pykew works fine. Thanks again! $\endgroup$ – Davide Jul 23 at 19:52
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The NCBI taxonomy is a quite extensive resource: https://www.ncbi.nlm.nih.gov/taxonomy

I would thus expect there is a good chance that it covers all of the taxa that you are interested in. It officially claims that it is not an authoritative source, but it's still pretty darned good.

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    $\begingroup$ Please note that you should take the NCBI seriously when they say it is not an authoritative resource. Orthography and synonymy are rarely up to date, and many accepted species are not present because they lack associated sequence data. $\endgroup$ – NatWH Jul 19 at 10:01

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