Sharing data with Open Tree of Life

In order for phylogenetic results to be incorporated into Open Tree of Life (and indeed, to be critically evaluated and incorporated into any downstream analysis), these data must be available digitally. In addition, phylogenetic trees must include sufficient metadata to a) replicate the analysis and b) evaluate the phylogenetic hypotheses. The Open Tree of Life requirements are a subset of the Minimum Information About a Phylogenetic Analysis (MIAPA) checklist. Note that these requirements will almost certainly evolve over time as the project progresses.

At minimium, Open Tree of Life requires:

  • citation information about the study (yes, this means that we only accept trees associated with publications)
  • a text file containing the phylogenetic tree in a machine-readable format (no PDFs, image files, Word documents)
  • meaningful labels on the tips of the tree: each tip of the tree must have a unique label that allows for mapping of the tip to an entry in a public database (NCBI taxonomy, GBIF classification or other online resource).
  • identification of the root: synthesizing phylogenetic data requires the tree to be correctly rooted (noting that this may not be possible for all phylogenies).
  • identification of the primary clade of interest: if the clade of interest for the study is more limited in scope than the entire ingroup. Relationships in the primary clade are assumed to be relationships that the author(s) presents as their phylogenetic result.

Other information from the MIAPA checklist greatly increases the usability of a phylogeny.

We have a publication in PLOS Currents Tree of Life with best practices for sharing phylogenetic data.

Our curation application allows you to upload and annotate phylogenetic data, both for Open Tree of Life synthesis and also to share widely for other downstream uses.

One response

  1. Pingback: Data sharing, OpenTree and GoLife | OPEN TREE OF LIFE

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s