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phylotastic / phylotastic-portal

Web tool (ruby on rails) providing access to phylotastic services for acquiring species trees.
https://github.com/phylotastic/phylotastic/wiki
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supporting studies explanation #291

Open arlin opened 7 years ago

arlin commented 7 years ago

The "supporting studies" feature is going to be confusing for users.

  1. (Arlin) Put an explanation in the Help-FAQ view.
  2. Make a float-over for the "Supporting studies" header that says "Published studies with trees relevant to deriving your Phylotastic tree (trees from OpenTree may lack supporting studies if they are based solely on taxonomy)."
  3. Replace the "no supporting studies" message with a message that says "No supporting studies were found. This typically happens when a tree is derived from the OpenTree taxonomy without phylogenetic refinement."
ducvan0212 commented 7 years ago

Done 2 and 3.

arlin commented 7 years ago

thanks @ducvan. your part is done. I will add the text for the FAQ soon.

arlin commented 7 years ago

FAQ changes. Add the text and construct the indicated HTML links.

  1. Add the question "What are supporting studies? Why are they sometimes missing?" with the answer: "Supporting studies are publications on which the tree is based. In the case of trees derived by subtree extraction from OpenTree's synthetic tree (supertree), the supporting studies provide the trees used to refine the taxonomy to make a supertree, by the method of Redelings and Holder, 2017 [LINK: https://peerj.com/preprints/2538/]. The studies listed for your subtree provide support for specific nodes in your subtree."

  2. Change the answer to "How is the tree made? Where does it come from?" to the following:

Phylotastic trees are retrieved from existing sources that store trees or merge them into supertrees. Currently all Phylotastic trees are based on the supertree developed by the OpenTree [LINK: https://tree.opentreeoflife.org] project (their "synthetic tree"). OpenTree begins with a taxonomy covering millions of species, and a database of curated "source trees". The source trees are then used to add phylogenetic information to the taxonomy, using the method of Redelings and Holder, 2017 [LINK: https://peerj.com/preprints/2538/].