Working with tree collections

A collection is a curated ordered list of trees. Any user can create a collection, add / delete trees to a collection, or modify the order. Collections are stored on github, which means that we have a full history of additions, deletions, and changes to any collection. You will need a GitHub account to create or edit a collection. The first time you log in, you will need to give OpenTree permission to associate your curation work with your GitHub account.

We use collections to manage the inputs to synthesis. At this point, there isn't much other functionality built into the web application for collections, but that is something that we are working on. Possibilities include custom synthesis, conflict statistics, or other analyses. Have a suggestion? Leave a new issue in the feedback repo.

You can browse the full list of collections on the collections page.

Adding a new collection

Adding trees to a collection

You can add trees from the collection window ('add tree X to this collection'), or from a study ('add this tree to collection X').

From the collections window

Click on any collection to open the collection window. Click the blue Edit button.

Click Add tree to this collection, at the bottom of the window to open up the add tree fields:

Enter either the studyID and treeID or the URL to the tree (you can get either one from the curator application). Note that the studyID includes the prefix (e.g. ot_234 or pg_264) and the tree ID may include tree at the start. Once you have entered the fields, click the blue plus button. A message at the bottom of the browser window will indicate if the tree has been added successfully or if there was an error.

Changing the order of trees in a collection

Deleting trees from a collection

Adding trees to synthesis

The four Inputs to synthesis collections are the lists of trees currently used to create the synthetic tree. If you want to include a tree in synthesis, add it to the appropriate collection. Adding a comment helps, too.