by Open Tree of Life developers (primarily Mark T. Holder, Emily Jane McTavish, Duke Leto, and Jim Allman)

Big Thanks to NSF!

• Python library
• implements much of the phylesystem-api
• manages local instances of the phylesystem
• call open tree web services for:
  • interacting with the "central" phylesystem-api
  • resolve names to the Open Tree Taxonomy
  • query against an estimate of the Tree of Life

• we've adopted a service oriented architecture.
• things have gotten a bit complex...

• come to the Tree-for-all hackathon!
• https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs
• note the "v1": ...org/treemachine/v1/getDraftTree...

• make accessing the API simpler and more "pythonic"
• improve stability - when the Open Tree of Life API version changes, the peyotl interface won't (hopefully)

• calling in "taxomachine" by Cody Hinchliff.

from peyotl.sugar import taxomachine
print taxomachine.TNRS('Anolis sagrei')

returns a object summarizing the possible matches.

from peyotl.sugar import treemachine as tm
o = [515698, 515712, 149491, 876340, 505091, 840022, 692350, 451182, 301424, 876348, 515698, 1045579, 267484, 128308, 380453, 678579, 883864, 863991, 3898562, 23821, 673540, 122251, 106729, 1084532, 541659]
r = tm.get_synth_tree_pruned(ott_ids=o)

returns the tree (currently only in an odd, in-house format called "Arguson")

• calling in "oti" by Cody Hinchliff.

from peyotl.sugar import oti
n = 'Aponogeoton ulvaceus'
print oti.find_trees(ottTaxonName=n)

returns a list of objects listing studyID and treeID

from peyotl.api import PhylesystemAPI
pa = PhylesystemAPI(get_from='api')
print pa.get('pg_10',
             tree_id='tree3',
             subtree_id='ingroup',
             format='newick')

pa = PhylesystemAPI(get_from='api',
                    transform='server')

pa = PhylesystemAPI(get_from='api',
                    transform='client')

pa = PhylesystemAPI(get_from='external')

pa = PhylesystemAPI(get_from='local')

t =  pa.get('pg_10',...

request tree

look up location of study NexSON file

read NexSON file

extract tree

convert to newick

return to client

request tree

look up location of study NexSON file

read NexSON file

return to client

extract tree

convert to newick

request tree

look up GitHub URL of study NexSON file

return to study NexSON client

extract tree

convert to newick

request tree

look up location of study NexSON file

read NexSON file

extract tree

convert to newick

In the phylesystem-API:

• the datastore is publicly accessible as the git repo (Emily Jane McTavish's talk)

• the library (peyotl) adding functionality to the data was designed to be a server-side and a client-side library.

I'm hoping that peyotl will be:

1. a useful tool for Python programmers,

2. a easy-to-grok entry point to the intimidating set of services offered by the Open Tree of Life effort.