Answers.Body: <p>Probably the best currently available online database is RBG Kew's <a href="http://www.plantsoftheworldonline.org/" rel="nofollow noreferrer">Plants of the World Online</a>. 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. </p>
  
  <p>Alternatively, there is <a href="http://www.worldfloraonline.org/" rel="nofollow noreferrer">World Flora Online</a>, replacing the now-defunct <a href="http://www.theplantlist.org/" rel="nofollow noreferrer">The Plant List v1.1</a>, which also integrates taxonomic data from a range of reliable sources and national lists. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-19T20:14:29.767Z
Answers.Text: Thanks! RBG Kew's site looks great, do you know if I can somehow download the data?
Answers.UserDisplayName: Davide Leonessi
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-20T09:47:47.857Z
Answers.Text: Hi @Davide - you should use the dedicated APIs: either [pykew](https://pypi.org/project/pykew/) for python, or [taxize](https://github.com/ropensci/taxize/) for R.
Answers.UserDisplayName: NatWH
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-22T15:18:09.417Z
Answers.Text: Thanks @NatWH, I'll look pykew up
Answers.UserDisplayName: Davide Leonessi
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-23T15:05:38.443Z
Answers.Text: 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...
Answers.UserDisplayName: Davide Leonessi
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-23T16:06:53.390Z
Answers.Text: @Davide pykew returns a search result as an iterator consisting of as many dictionary-like elements as your search term has hits. Try this fragment to get the family associated with each record: `res = powo.search({Name.genus: 'Poa'})` followed by `[ r['family'] for r in res ]`. Irritatingly (but understandably), `powo.search()` returns a generator rather than an iterator, so you will have to rerun the search if you want to operate on the same results again.
Answers.UserDisplayName: NatWH
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-23T18:02:21.307Z
Answers.Text: Thank you @NatWH, now I manage to get some results! While running, I received an error when using your code for the genus 'Zizyphus'. I get " 'SearchResult' object has no attribute '_results' ". I imagine that such genus is not in the Kew database - in this case how can I tell the code to ignore the error and just return something like 'Unassigned'?
Answers.UserDisplayName: Davide Leonessi
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-23T19:52:16.633Z
Answers.Text: Actually realised that my data is not perfect: the correct spelling of that genus is 'Ziziphus' - pykew works fine. Thanks again!
Answers.UserDisplayName: Davide Leonessi
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-19T10:07:46.943Z
Answers.LastActivityDate: 2019-07-19T10:07:46.943Z
Answers.UserDisplayName: NatWH
Answers.Body: <p>The NCBI taxonomy is a quite extensive resource: <a href="https://www.ncbi.nlm.nih.gov/taxonomy" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/taxonomy</a></p>
  
  <p>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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-19T10:01:58.407Z
Answers.Text: 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.
Answers.UserDisplayName: NatWH
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-19T00:33:16.833Z
Answers.LastActivityDate: 2019-07-19T00:33:16.833Z
Answers.UserDisplayName: jakebeal
Body: <p>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.</p>
  
  <p>I found a long but not exhaustive list on Wikipedia:
  <a href="https://en.wikipedia.org/wiki/List_of_trees_and_shrubs_by_taxonomic_family" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/List_of_trees_and_shrubs_by_taxonomic_family</a></p>
  
  <p>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)</p>
  
  <p>Does anyone know if such a crosswalk file exists, in some scientific article or somewhere in the Internet?</p>
  
  <p>Moreover, please tell me if there are other StackExchange websites which could be more appropriate, I wasn't sure of where to post this.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-18T23:10:40.303Z
Comments.Text: Contact Kew. BTW when emailing them make sure you call them genera.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-22T15:17:26.530Z
Comments.Text: Thanks, it is always good to learn something new!
Comments.UserDisplayName: Davide Leonessi
Tags: <database><public-databases><taxonomy>
Title: Looking for a taxonomic dataset that links tree genera (or species) to families
ThreadText: # Looking for a taxonomic dataset that links tree genera (or species) to families
  
  (Asked by: username_0 on 2019-07-18)
  
  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.
  
  **Tags:** database, public-databases, taxonomy
  
  > **Comments:**
  > **username_1**: Contact Kew. BTW when emailing them make sure you call them genera.  
  > **username_0**: Thanks, it is always good to learn something new!  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2019-07-19. Score: 2 | Accepted answer
  
  Probably the best currently available online database is RBG Kew's [Plants of the World Online](http://www.plantsoftheworldonline.org/). 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](http://www.worldfloraonline.org/), replacing the now-defunct [The Plant List v1.1](http://www.theplantlist.org/), which also integrates taxonomic data from a range of reliable sources and national lists.
  
  > **Comments:**
  > **username_0**: Thanks! RBG Kew's site looks great, do you know if I can somehow download the data?  
  > **username_2**: Hi @username_0 - you should use the dedicated APIs: either [pykew](https://pypi.org/project/pykew/) for python, or [taxize](https://github.com/ropensci/taxize/) for R.  
  > **username_0**: Thanks @username_2, I'll look pykew up  
  > **username_0**: Hey @username_2, 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...  
  > **username_2**: @username_0 pykew returns a search result as an iterator consisting of as many dictionary-like elements as your search term has hits. Try this fragment to get the family associated with each record: `res = powo.search({Name.genus: 'Poa'})` followed by `[ r['family'] for r in res ]`. Irritatingly (but understandably), `powo.search()` returns a generator rather than an iterator, so you will have to rerun the search if you want to operate on the same results again.  
  > **username_0**: Thank you @username_2, now I manage to get some results! While running, I received an error when using your code for the genus 'Zizyphus'. I get " 'SearchResult' object has no attribute '_results' ". I imagine that such genus is not in the Kew database - in this case how can I tell the code to ignore the error and just return something like 'Unassigned'?  
  > **username_0**: Actually realised that my data is not perfect: the correct spelling of that genus is 'Ziziphus' - pykew works fine. Thanks again!  
  
  ---
  
  ### Answer by username_3 on 2019-07-19. Score: 4
  
  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.
  
  > **Comments:**
  > **username_2**: 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.  
  
  ---
  
  