Community contributed phylogenies

• 6745 trees from 2914 published studies
• 1188 trees from 991 studies partly curated
• 335 trees from 327 studies completely curated and included in the synthetic tree.

Smith, Cranston et al. Submitted

• Large data set: Thousands of phylogenies, and always growing (hopefully!)
• Each phylogeny requires some hand curation, often by multiple people
• Need to be readily accessible, and editable by interested researchers
  
  
  

Smith, Cranston et al. Submitted

• SQL database
• Mongo, couchDB
• git/github

• Trees and annotations by study in Nexson format
  (JSON serialization of NeXML)
• Whole datastore is a git repo!

• Work in progress branch is created upon curation
• If study hasn't been edited by someone else, changes are automatically merged.
• Otherwise, merged changes are returned to curator to accept or reject
• Updates pushed to GitHub after each commit

Features

• Tracking curation attribution
• Some subjective choices, edits made by many in the community over time

• These trees are the backend for OpenTree showpiece

the synthetic tree!

• but also a useful datastore for other researchers
• Repo is hosted on GitHub, entire data store can be easily cloned and updated
• Anyone can easily download all the data!

• Hosting on Github
• Free
• Familar to many in the field

• Phylogenies are hard to diff - e.g. rerooting changes everything!
• Nexson are not a line based format
• Repo size limits on github

• Semantic diffs
• Pull requests

github.com/OpenTreeOfLife/phylesystem-1

- Maybe! Any of the OpenTree software team are happy to chat about pros and cons.

Mark Holder
University of Kansas
OpenTree of Life project
Especially the Software team
NSF AVATOL #1208809