Collecting input trees

One of the first steps is to collect published phylogenies to include in the first draft tree of life. In advance of having an interface for annotation and input of data, we are starting by collecting a list of publications using a public Mendeley group.

Adding publications to the list
The first step is to create a Mendeley account, if you don’t already have one. Then, join the OpenTree Mendeley group. There are a few ways to add papers to the group:

  • use the web importer: when you add a paper to your library, you can choose to also add it to a group
  • in Mendeley desktop: simply drag a paper from your library into the group
  • from your library on the Mendeley site: select the checkboxes beside the papers in your library, then choose ‘OpenTree’ from pulldown ‘Add selected documents to…’ list.

Tagging papers if data available
We can only include a published phylogeny in the draft tree of life if the data (tree and alignment files) is available. We are using a couple of tags to track data availability. Feel free to use other tags, but please document how you are using them.

  • treebase: the data is in TreeBASE
  • datadryad: the data is in Dryad
  • nodata: we can’t find any data deposited in either repository 😦

Metadata for trees
In addition to the tree in digital format, we would like to have metadata about the input trees (what data underlies the tree? how was it built?). We are talking to the MIAPA folks about defining and collecting metadata. There is a public metadata document where we are keeping notes.

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