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biotaphy / ot_service_wrapper

Client library for Open Tree of Life services used in the Biotaphy project
GNU General Public License v3.0
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Open Tree link #1

Open snacktavish opened 4 years ago

snacktavish commented 4 years ago

(moved from https://github.com/biotaphy/analyses/issues/67) Ah interesting! I can definitely help with the service call, and do manage the production server, as well as ot38, along with @mtholder, @kcranston, and @bredelings - but currently the OpenTree API doesn't return branch lengths on development servers (ot38) or production. We are working on adding time estimates to nodes, but given that many of the relationships are derived from taxonomy, that isn't straightforward.

cjgrady commented 4 years ago

That server has been working for us for a while and producing branch lengths. @blackrim had set it up for us. The BiotaPhy project has several analyses that require branch lengths and a few that require trees to be ultrametric. We have been using the follow command to retrieve trees for user provided OpenTree ids:

$ curl -X POST -H "Content-Type: application/json" -d '{"ott_ids": [292466, 267845, 316878, 102710], "label_format": "id"}' http://141.211.236.35:10999/induced_subtree

returns:

{"newick":"(((((((((((((((((((((((((((((ott267845:9.49775)ott496027:25.5830937415)mrcaott1566ott496009:1.46054421769)mrcaott1566ott2175:1.46054421769)mrcaott1566ott5934:1.46054421769)mrcaott246ott1566:1.7502437415)mrcaott246ott3364:0.786490952381)mrcaott246ott1488:1.07619047619)mrcaott246ott10351:1.07619047619)mrcaott246ott193904:1.07619047619)mrcaott246ott4820:0)mrcaott246ott191995:0.56208)mrcaott246ott32658:1.04)mrcaott246ott5929:28.5786558491)mrcaott246ott44866:1.63773584906)mrcaott246ott428578:1.63773584906)mrcaott246ott3212:1.63773584906)ott1041547:1.63773584906)mrcaott246ott7113:1.63773584906)mrcaott246ott47588:1.63773584906)mrcaott246ott3600042:1.63773584906)mrcaott246ott2907:0)mrcaott246ott1858:0)mrcaott246ott928360:0)mrcaott246ott5272:0)mrcaott246ott7145:0)mrcaott246ott5021:0.0322832973806)mrcaott246ott5481:243.448177534,(((((((((((((ott102710:13.097330757567)mrcaott53700ott466627:0.795214545455)mrcaott53700ott572162:6.70985857143)mrcaott4765ott53700:1.71681857143)mrcaott4765ott51354:1.71681857143)mrcaott4765ott415487:7.27728411765)mrcaott4765ott49310:2.08732411765)mrcaott4765ott49319:2.08732411765)mrcaott4765ott54193:12.7158483333)mrcaott4765ott151684:0.000142631578953)mrcaott4765ott104461:25.2011005)mrcaott4765ott75785:0.000608571428572)ott837585:10.3037359091,((((((ott316878:37.0714367252)mrcaott166683ott316879:4.63392959064)mrcaott30843ott166683:2.45325684211)mrcaott30843ott75874:2.45325684211)ott765193:27.3580225)mrcaott30843ott714464:9.7302647619)ott241841:0.0000459090909004)ott5839486:246.536935742)ott241846:5.49770753425,(((ott292466:53.700006)ott857849:17.900002)ott857847:17.900002)ott81443:246.233424715)ott81461;","unmatched_ott_ids":[]}

blackrim commented 4 years ago

Just to chime in, this is obviously not an official server for opentree but instead maintained internally for the biotaphy project because of the requirements for branch lengths within biotaphy. So it takes the synth tree from open tree and applies dates from timetree. But of course when opentree can serve branch lengths, we will just point to the official server.