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Open Tree of Life APIs
josephwb edited this page Sep 16, 2014
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Do not edit this page! The API documentation is automatically generated using code in the opentree repo. If you have a suggestion to improve this documentation, please submit an issue on the feedback repo.
This documentation describes version 2.0 of the Open Tree of Life APIs. There is also documentation for version 1.0, which is still active but is deprecated and will eventually be retired.
The Open Tree of Life APIs include services to access the following types of data:
Tree of life : the single draft tree of life that is a combination of the source trees and the opentree reference taxonomy.
Graph of life : the neo4j graph database used to build the synthetic tree; contains additional nodes and edges (from taxonomy & source trees) that are not in the synthetic tree.
Taxonomic name resolution services : methods for resolving taxonomic names to Open Tree of Life Taxonomy identifiers (ott ids).
Taxonomy : the opentree taxonomy (OTT), which is a synthesis of different input taxonomies.
Studies containing source trees : extracted primarily from the scientific literature, containing the source trees used to build the draft tree of life.
The base URL for all services:
http://api.opentreeoflife.org/v2
Caveats
- the JSON return values are not consistent between software components. We are working to standardize on the documented NexSON format.
- neo4j implements POST for some methods that really should be GET.
Questions / Comments
If you have questions, or have a problem with any of these methods, please leave an issue in the feedback issue tracker.
Methods to access information about and representations of the (current) draft tree of life. These methods do not accept taxon names as input, but instead require either:
- Open Tree Taxonomy identifiers (ott ids), which can be determined by using the taxonomic name resolution services, or
- Graph of life node ids, which can be determined using various methods such as mrca.
Detailed descriptions for each method follow below the summary table.
| URL | Verb | Summary |
|---|---|---|
/tree_of_life/about |
POST | Return information about the current draft tree itself. |
/tree_of_life/mrca |
POST | Return the most recent common ancestor of a set of nodes in the draft tree. |
/tree_of_life/subtree |
POST | Return the complete subtree below a given node. |
/tree_of_life/induced_subtree |
POST | Return the induced subtree on the draft tree that relates a set of nodes. |
Return information about the current draft tree itself.
POST /tree_of_life/about
Returns summary information about the current draft tree of life, including information about the list of source trees and the taxonomy used to build it.
Parameters with bold type definitions are required.
study_list : boolean
Return a list of source studies
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/tree_of_life/aboutExample result:
{
"root_node_id" : 132,
"study_list" : [ {
"study_id" : "pg_2827",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6577"
}, {
"study_id" : "pg_761",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1415"
}, {
"study_id" : "pg_77",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5878"
}, {
"study_id" : "pg_754",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1392"
}, {
"study_id" : "pg_330",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "325"
}, {
"study_id" : "pg_1131",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2265"
}, {
"study_id" : "pg_2608",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6288"
}, {
"study_id" : "pg_2539",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6294"
}, {
"study_id" : "pg_2645",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6165"
}, {
"study_id" : "pg_2644",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6164"
}, {
"study_id" : "pg_2642",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6161"
}, {
"study_id" : "pg_2626",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6142"
}, {
"study_id" : "pg_332",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "333"
}, {
"study_id" : "pg_2832",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6586"
}, {
"study_id" : "pg_1866",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3765"
}, {
"study_id" : "pg_59",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5731"
}, {
"study_id" : "pg_704",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1266"
}, {
"study_id" : "pg_2638",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6157"
}, {
"study_id" : "pg_1974",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4038"
}, {
"study_id" : "pg_1974",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4039"
}, {
"study_id" : "pg_2901",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6721"
}, {
"study_id" : "pg_2906",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6730"
}, {
"study_id" : "pg_1524",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3046"
}, {
"study_id" : "pg_1414",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2837"
}, {
"study_id" : "pg_1411",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5110"
}, {
"study_id" : "pg_1409",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2822"
}, {
"study_id" : "pg_1408",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2821"
}, {
"study_id" : "pg_1407",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2818"
}, {
"study_id" : "pg_1401",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2812"
}, {
"study_id" : "pg_1391",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2795"
}, {
"study_id" : "pg_1434",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2876"
}, {
"study_id" : "pg_2633",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6153"
}, {
"study_id" : "pg_1539",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3088"
}, {
"study_id" : "pg_2634",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6154"
}, {
"study_id" : "pg_1022",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1967"
}, {
"study_id" : "pg_562",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "817"
}, {
"study_id" : "pg_588",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "878"
}, {
"study_id" : "pg_2048",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4220"
}, {
"study_id" : "pg_1137",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2295"
}, {
"study_id" : "pg_62",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2878"
}, {
"study_id" : "pg_2841",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6597"
}, {
"study_id" : "pg_2085",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4317"
}, {
"study_id" : "pg_180",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "794"
}, {
"study_id" : "pg_576",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "849"
}, {
"study_id" : "pg_581",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "859"
}, {
"study_id" : "pg_582",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "862"
}, {
"study_id" : "pg_598",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "926"
}, {
"study_id" : "pg_599",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "927"
}, {
"study_id" : "pg_603",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "940"
}, {
"study_id" : "pg_721",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1298"
}, {
"study_id" : "pg_723",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1300"
}, {
"study_id" : "pg_921",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4103"
}, {
"study_id" : "pg_61",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "816"
}, {
"study_id" : "pg_573",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "839"
}, {
"study_id" : "pg_566",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "832"
}, {
"study_id" : "pg_1522",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3044"
}, {
"study_id" : "pg_1570",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3142"
}, {
"study_id" : "pg_1583",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3194"
}, {
"study_id" : "pg_1572",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3145"
}, {
"study_id" : "pg_2909",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6735"
}, {
"study_id" : "pg_43",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3862"
}, {
"study_id" : "pg_38",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1750"
}, {
"study_id" : "pg_2878",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6673"
}, {
"study_id" : "pg_2624",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6139"
}, {
"study_id" : "pg_2128",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4437"
}, {
"study_id" : "pg_1102",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2177"
}, {
"study_id" : "pg_1129",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2251"
}, {
"study_id" : "pg_1109",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2201"
}, {
"study_id" : "pg_2004",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4118"
}, {
"study_id" : "pg_53",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1280"
}, {
"study_id" : "pg_1118",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2226"
}, {
"study_id" : "pg_2669",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6213"
}, {
"study_id" : "pg_2032",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5922"
}, {
"study_id" : "pg_1901",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "3877"
}, {
"study_id" : "pg_713",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "1287"
}, {
"study_id" : "pg_2912",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6740"
}, {
"study_id" : "pg_259",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "142"
}, {
"study_id" : "pg_264",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "150"
}, {
"study_id" : "pg_267",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "161"
}, {
"study_id" : "pg_2077",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4291"
}, {
"study_id" : "pg_293",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "201"
}, {
"study_id" : "pg_197",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "784"
}, {
"study_id" : "pg_595",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "896"
}, {
"study_id" : "pg_131",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6236"
}, {
"study_id" : "pg_2689",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6241"
}, {
"study_id" : "pg_597",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "906"
}, {
"study_id" : "pg_2001",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4100"
}, {
"study_id" : "pg_606",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5290"
}, {
"study_id" : "pg_270",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "159"
}, {
"study_id" : "pg_596",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "901"
}, {
"study_id" : "pg_294",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "202"
}, {
"study_id" : "pg_292",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "199"
}, {
"study_id" : "pg_58",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "775"
}, {
"study_id" : "pg_548",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "798"
}, {
"study_id" : "pg_2055",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4234"
}, {
"study_id" : "pg_2057",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4240"
}, {
"study_id" : "pg_2127",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4426"
}, {
"study_id" : "pg_594",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "890"
}, {
"study_id" : "pg_261",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "145"
}, {
"study_id" : "pg_57",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "777"
}, {
"study_id" : "pg_1087",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2114"
}, {
"study_id" : "pg_1087",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2115"
}, {
"study_id" : "pg_2690",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6243"
}, {
"study_id" : "pg_2045",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4213"
}, {
"study_id" : "pg_605",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "947"
}, {
"study_id" : "pg_271",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5017"
}, {
"study_id" : "pg_2661",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6198"
}, {
"study_id" : "pg_2052",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4228"
}, {
"study_id" : "pg_1103",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2178"
}, {
"study_id" : "pg_14",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "12"
}, {
"study_id" : "pg_2598",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6020"
}, {
"study_id" : "pg_2000",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "4098"
}, {
"study_id" : "pg_20",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2162"
}, {
"study_id" : "pg_1101",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2172"
}, {
"study_id" : "pg_2565",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5708"
}, {
"study_id" : "pg_1094",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "2138"
}, {
"study_id" : "pg_2641",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6160"
}, {
"study_id" : "pg_99",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "5885"
}, {
"study_id" : "pg_93",
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"study_id" : "taxonomy",
"git_sha" : "",
"tree_id" : ""
} ],
"root_taxon_name" : "cellular organisms",
"num_source_studies" : 484,
"taxonomy_version" : "2.8_5",
"root_ott_id" : 93302,
"num_tips" : 2339460,
"date" : "Sun Sep 14 01:27:06 EDT 2014",
"tree_id" : "otol.draft.22"
}Return the most recent common ancestor of a set of nodes in the draft tree.
POST /tree_of_life/mrca
Get the MRCA of a set of nodes on the current draft tree. Accepts any combination of node ids and ott ids as input. Returns information about the most recent common ancestor (MRCA) node as well as the most recent taxonomic ancestor (MRTA) node (the closest taxonomic node to the MRCA node in the synthetic tree; the MRCA and MRTA may be the same node). Node ids that are not in the synthetic tree are dropped from the MRCA calculation. For a valid ott id that is not in the synthetic tree (i.e. it is not recovered as monophyletic from the source tree information), the taxonomic descendants of the node are used in the MRCA calculation. Returns any unmatched node ids / ott ids.
Parameters with bold type definitions are required.
node_ids : longs
A set of node ids
ott_ids : longs
A set of ott ids
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/tree_of_life/mrca -H "content-type:application/json" -d '{"ott_ids":[412129, 536234]}'Example result:
{
"mrca_name" : "",
"nearest_taxon_mrca_rank" : "superorder",
"mrca_rank" : "",
"nearest_taxon_mrca_ott_id" : 241846,
"invalid_node_ids" : [ ],
"nearest_taxon_mrca_node_id" : 3019669,
"ott_ids_not_in_tree" : [ ],
"nearest_taxon_mrca_unique_name" : "Neognathae",
"ott_id" : "null",
"mrca_node_id" : 3853463,
"mrca_unique_name" : "",
"nearest_taxon_mrca_name" : "Neognathae",
"node_ids_not_in_tree" : [ ],
"invalid_ott_ids" : [ ]
}Return the complete subtree below a given node.
POST /tree_of_life/subtree
Return a complete subtree of the draft tree descended from some specified node. The node to use as the start node may be specified using either a node id or an ott id, but not both. If the specified node is not in the synthetic tree (or is entirely absent from the graph), an error will be returned.
Parameters with bold type definitions are required.
node_id : long
The node id of the node in the tree that should serve as the root of the tree returned. This argument may not be used in combination with ott_id.
ott_id : long
The ott id of the node in the tree that should serve as the root of the tree returned. This argument may not be used in combination with node_id.
tree_id : string
The identifier for the synthesis tree. We currently only support a single draft tree in the db at a time, so this argument is superfluous and may be safely ignored.
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/tree_of_life/subtree -H "content-type:application/json" -d '{"ott_id":3599390}'Example result:
{
"newick" : "((Teretistris_fornsi_ott3597217,Teretistris_fernandinae_ott449562)Teretistris_ott808916,Seiurus_aurocapilla_ott285207,(Dendroica_subita_ott3597234,Dendroica_aestiva_ott3597233,Dendroica_delicata_ott3597229,Dendroica_flavescens_ott3597236)Dendroica_ott666104,(Chloris_spinoides_ott4947620,Chloris_sinica_ott4947618,Chloris_monguilloti_ott4947617,Chloris_ambigua_ott4947619)Chloris_ott4947616,((((Seiurus_novaeboracensis_ott4132022,Seiurus_motacilla_ott4132023),(((Mniotilta_varia_ott757859)Mniotilta_ott309802,((Limnothlypis_swainsonii_ott1024615)Limnothlypis_ott1024616,(Protonotaria_citrea_ott285212)Protonotaria_ott285204)),(Vermivora_cyanoptera_ott3597221,(Vermivora_chrysoptera_ott85249,Vermivora_pinus_ott85247),Vermivora_bachmanii_ott237566)Vermivora_ott150638)),((((Oreothlypis_peregrina_ott430151,((Oreothlypis_crissalis_ott85251,(Oreothlypis_luciae_ott711624,((Oreothlypis_ruficapilla_ridgwayi_ott900162,Oreothlypis_ruficapilla_ruficapilla_ott1001290)Oreothlypis_ruficapilla_ott392341,Oreothlypis_virginiae_ott759416))),(Vermivora_celata_lutescens_ott669574)Oreothlypis_celata_ott88835)),(Oreothlypis_gutturalis_ott956238,Oreothlypis_superciliosa_ott430147))Oreothlypis_ott4947615,(((Oporornis_agilis_ott659603)Oporornis_ott119886,(Leucopeza_semperi_ott636990)Leucopeza_ott636993),(Geothlypis_chiriquensis_ott3597227,Geothlypis_auricularis_ott3597223,((Geothlypis_tolmiei_ott3597226,Geothlypis_philadelphia_ott3597222),(Geothlypis_aequinoctialis_ott669575,Geothlypis_poliocephala_ott63586)),Geothlypis_velata_ott3597224,(((((Geothlypis_trichas_ott998127,Geothlypis_nelsoni_ott63582,Geothlypis_flavovelata_ott63583),Geothlypis_rostrata_ott375821),Geothlypis_beldingi_ott63581),(Geothlypis_semiflava_ott636992,Geothlypis_speciosa_ott85253)),Geothlypis_formosa_ott3597225))Geothlypis_ott998126)),((((Basileuterus_conspicillatus_ott384904,Basileuterus_chrysogaster_ott384910,Basileuterus_basilicus_ott405179,Basileuterus_leucophrys_ott317448,Basileuterus_fulvicauda_ott357657,Basileuterus_signatus_ott1034068,Basileuterus_rivularis_ott817143,Basileuterus_nigrocristatus_ott5620,(Basileuterus_luteoviridis_euophrys_ott578348,Basileuterus_luteoviridis_luteoviridis_ott5626,Basileuterus_luteoviridis_striaticeps_ott5625)Basileuterus_luteoviridis_ott1034069,(((Basileuterus_trifasciatus_ott384908,(Basileuterus_tristriatus_auricularis_ott1034074)Basileuterus_tristriatus_ott117643),((Basileuterus_culicivorus_austerus_ott508026,Basileuterus_culicivorus_auricapilla_ott813148,Basileuterus_culicivorus_flavescens_ott289268,Basileuterus_culicivorus_culicivorus_ott289274,Basileuterus_culicivorus_azarae_ott289272)Basileuterus_culicivorus_ott508027,Basileuterus_hypoleucus_ott384914)),((Basileuterus_rufifrons_mesocrysus_ott1034067)Basileuterus_rufifrons_ott1034070,(Basileuterus_belli_ott410568,Basileuterus_melanogenys_ott384916))),Basileuterus_lachrymosus_ott3597220,Basileuterus_culicivorus_x_Basileuterus_hypoleucus_ott4947614,Basileuterus_bivittatus_ott994339,Basileuterus_ignotus_ott3597219,Basileuterus_flaveolus_ott865397,Basileuterus_griseiceps_ott3597218,Basileuterus_chlorophrys_ott301266,(Basileuterus_coronatus_regulis_ott508024)Basileuterus_coronatus_ott508025,Basileuterus_leucoblepharus_ott292918,(Basileuterus_cinereicollis_pallidulus_ott508022)Basileuterus_cinereicollis_ott508023,Basileuterus_fraseri_ott384906)Basileuterus_ott758213,((Cardellina_canadensis_ott3597182,(Cardellina_pusilla_ott3597185,((Cardellina_versicolor_ott3597184,Cardellina_rubra_ott3597183),Cardellina_rubrifrons_ott1061912)))Cardellina_ott5266838,(Myioborus_castaneocapillus_ott315418,(((((Myioborus_albifrons_ott85245,(Myioborus_melanocephalus_ott315419,Myioborus_ornatus_ott449735)),Myioborus_flavivertex_ott992009),(Myioborus_torquatus_ott992006,(Myioborus_pariae_ott992008,(Myioborus_albifacies_ott659607,(Myioborus_cardonai_ott992007,Myioborus_castaneocapilla_ott3597186))))),Myioborus_brunniceps_ott859999),Myioborus_miniatus_ott859998),Myioborus_pictus_ott285205)Myioborus_ott886174)),(Myiothlypis_griseiceps_ott3599568,((((Myiothlypis_flaveolus_ott3599765,Myiothlypis_leucoblepharus_ott3599810),Myiothlypis_leucophrys_ott3599780),((Myiothlypis_fulvicauda_ott3599607,Myiothlypis_rivularis_ott3599526),(Myiothlypis_nigrocristatus_ott3599882,Myiothlypis_signatus_ott3599512))),Myiothlypis_luteoviridis_ott3599766),(Myiothlypis_bivittatus_ott3599828,((Myiothlypis_cinereicollis_ott3599528,Myiothlypis_conspicillatus_ott3599392),(Myiothlypis_fraseri_ott3599779,Myiothlypis_coronatus_ott3599881))))Myiothlypis_ott3599393),(((Setophaga_plumbea_ott3597205,(Setophaga_angelae_ott3597191,Setophaga_pharetra_ott3597190)),(Setophaga_citrina_ott3597211,(Setophaga_ruticilla_ott285200,(((Setophaga_caerulescens_ott3597187,((Setophaga_palmarum_ott3597202,((Setophaga_dominica_ott3597194,(Setophaga_coronata_coronata_ott349904,Setophaga_coronata_goldmani_ott870777,Setophaga_coronata_nigrifrons_ott870775,Setophaga_coronata_auduboni_ott870781)Setophaga_coronata_ott3597200),(Setophaga_pinus_ott3597210,Setophaga_pityophila_ott3597214))),(((((Setophaga_occidentalis_ott3597213,Setophaga_townsendi_ott3597215),(Setophaga_virens_ott3597195,Setophaga_chrysoparia_ott3597192)),(Setophaga_nigrescens_ott3597216,Setophaga_graciae_ott455853)),(Setophaga_adelaidae_ott3597207,(Setophaga_subita_ott3597204,Setophaga_delicata_ott3597206))),((Setophaga_vitellina_vitellina_ott478049,Setophaga_vitellina_crawfordi_ott478050)Setophaga_vitellina_ott3597196,Setophaga_discolor_ott3597197)))),((((Setophaga_pensylvanica_ott3597208,Setophaga_striata_ott60236),(Setophaga_petechia_ruficapilla_ott22843,Setophaga_petechia_aurifrons_ott862432,Setophaga_petechia_melanoptera_ott22846,Setophaga_petechia_aureola_ott790184,Setophaga_petechia_albicollis_ott22840,Setophaga_petechia_cruciana_ott22834,Setophaga_petechia_peruviana_ott22849,Setophaga_petechia_eoa_ott22856,Setophaga_petechia_bartholemica_ott22837,Setophaga_petechia_xanthotera_ott328787,Setophaga_petechia_babad_ott328784,Setophaga_petechia_gundlachi_ott22853,Setophaga_petechia_rhizophorae_ott328778,Setophaga_petechia_aestiva_ott612073,Setophaga_petechia_cienagae_ott328790,Setophaga_petechia_petechia_ott612062,Setophaga_petechia_castaneiceps_ott872016,Setophaga_petechia_aequatorialis_ott853391,Setophaga_petechia_chrysendeta_ott328781,Setophaga_petechia_erithachorides_ott612070,Setophaga_petechia_paraguanae_ott328794)Setophaga_petechia_ott612066),(Setophaga_fusca_ott3597193,Setophaga_castanea_ott3597188)),Setophaga_magnolia_ott3597209)),(Setophaga_kirtlandii_ott3597203,(Setophaga_tigrina_ott3597199,((Setophaga_americana_ott3597189,Setophaga_pitiayumi_ott3597201),Setophaga_cerulea_ott3597212)))))),Setophaga_flavescens_ott3597198)Setophaga_ott285198,(Catharopeza_bishopi_ott335225)Catharopeza_ott335224)))),(Helmitheros_vermivorum_ott860003)Helmitheros_ott886630),Setophaga_petechia_x_Geothlypis_trichas_ott4947613,(Icteria_virens_ott998133)Icteria_ott998132,(Zeledonia_coronata_ott449580)Zeledonia_ott449581,(Xenoligea_montana_ott808917)Xenoligea_ott808918,(Microligea_palustris_ott309808)Microligea_ott757867,(Granatellus_pelzelni_ott335232,Granatellus_venustus_ott972935,Granatellus_sallaei_ott972938)Granatellus_ott335231)Parulidae_ott3599390;",
"tree_id" : "otol.draft.22"
}Return the induced subtree on the draft tree that relates a set of nodes.
POST /tree_of_life/induced_subtree
Return a tree with tips corresponding to the nodes identified in the input set(s), that is consistent with topology of the current draft tree. This tree is equivalent to the minimal subtree induced on the draft tree by the set of identified nodes. Any combination of node ids and ott ids may be used as input. Nodes or ott ids that do not correspond to any found nodes in the graph, or which are in the graph but are absent from the synthetic tree, will be identified in the output (but will of course not be present in the resulting induced tree). Branch lengths in the result may be arbitrary, and the leaf labels of the tree may either be taxonomic names or (for nodes not corresponding directly to named taxa) node ids.
WARNING: there is currently a known bug if any of the input nodes is the parent of another, the returned tree may be incorrect. Please avoid this input case.
Parameters with bold type definitions are required.
node_ids : longs
Node ids indicating nodes to be used as tips in the induced tree
ott_ids : longs
OTT ids indicating nodes to be used as tips in the induced tree
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/tree_of_life/induced_subtree -H "content-type:application/json" -d '{"ott_ids":[292466, 501678, 267845, 666104, 316878, 102710, 176458]}'Example result:
{
"subtree" : "(((Stellula_ott501678,(Dendroica_ott666104,Cinclus_ott267845)),(Clangula_ott316878,Perdix_ott102710))Neognathae_ott241846,Struthio_ott292466)Aves_ott81461;",
"ott_ids_not_in_tree" : [ 176458 ],
"ott_ids_not_in_graph" : [ ],
"node_ids_not_in_graph" : [ ],
"node_ids_not_in_tree" : [ ]
}When we construct the tree of life, we load the taxonomy and input trees (a subset of the trees in the study database) into a neo4j graph database. Due to conflict between trees and taxonomy and the fact that the tree of life is binary, the graph contains nodes and edges not in the tree of life. These methods access the full graph database.
| URL | Verb | Summary |
|---|---|---|
/graph/about |
POST | Get information about the graph of life itself. |
/graph/source_tree |
POST | Return a source tree (including metadata) from the graph of life. |
/graph/node_info |
POST | Get information about a node in the graph of life. |
Get information about the graph of life itself.
POST /graph/about
Returns summary information about the entire graph database, including identifiers for the taxonomy and source trees used to build it.
Parameters with bold type definitions are required.
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/graph/aboutExample result:
{
"graph_num_source_trees" : 484,
"graph_taxonomy_version" : "2.8_5",
"graph_num_tips" : 2339516,
"graph_root_name" : "life",
"graph_root_node_id" : 1,
"graph_root_ott_id" : 805080
}Return a source tree (including metadata) from the graph of life.
POST /graph/source_tree
Returns a source tree (corresponding to a tree in some study) as it exists within the graph. Although the result of this service is a tree corresponding directly to a tree in a study, the representation of the tree in the graph may differ slightly from its canonical representation in the study, due to changes made during tree import (for example, pruning tips from the tree that cannot be mapped to taxa in the graph). In addition, both internal and terminal nodes are labelled ott ids. The tree is returned in newick format.
Parameters with bold type definitions are required.
git_sha : string
The git SHA identifying a particular source version.
study_id : string
The study identifier. Will typically include a prefix ("pg_" or "ot_")
tree_id : string
The tree identifier for a given study.
format : string
The name of the return format. The only currently supported format is newick.
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/graph/source_tree -H "content-type:applicatin/json" d '{"study_id":"pg_420", "tree_id":"522", "git_sha":"a2c48df995ddc9fd208986c3d4225112550c8452"}'Example result:
{
"message" : "Mandatory argument \"study_id\" not supplied.",
"exception" : "IllegalArgumentException",
"fullname" : "java.lang.IllegalArgumentException",
"stacktrace" : [ "org.neo4j.server.plugins.ParameterExtractor.extract(ParameterExtractor.java:47)", "org.neo4j.server.plugins.PluginMethod.invoke(PluginMethod.java:53)", "org.neo4j.server.plugins.PluginManager.invoke(PluginManager.java:168)", "org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:300)", "org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:122)", "java.lang.reflect.Method.invoke(Method.java:606)", "org.neo4j.server.rest.security.SecurityFilter.doFilter(SecurityFilter.java:112)" ]
}--_curl_--"study_id":"pg_420"
--_curl_-- "tree_id":"522"
--_curl_-- "git_sha":"a2c48df995ddc9fd208986c3d4225112550c8452"
Get information about a node in the graph of life.
POST /graph/node_info
Returns summary information about a node in the graph. The node of interest may be specified using either a node id, or an ott id, but not both. If the specified node or ott id is not in the graph, an error will be returned.
Parameters with bold type definitions are required.
include_lineage : boolean
Include the ancestral lineage of the node in the draft tree. If this argument is true, then a list of all the ancestors of this node in the draft tree, down to the root of the tree itself, will be included in the results. Higher list indices correspond to more incluive (i.e. deeper) ancestors, with the immediate parent of the specified node occupying position 0 in the list.
node_id : long
The node id of the node of interest. This argument may not be combined with ott_id.
ott_id : long
The ott id of the node of interest. This argument may not be combined with node_id.
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/graph/node_info -H "content-type:application/json" -d '{"ott_id":810751}'Example result:
{
"synth_sources" : [ {
"study_id" : "pg_2853",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6624"
}, {
"study_id" : "taxonomy",
"git_sha" : "",
"tree_id" : ""
}, {
"study_id" : "pg_420",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "522"
} ],
"in_synth_tree" : true,
"rank" : "family",
"in_graph" : true,
"name" : "Trochilidae",
"num_tips" : 371,
"ott_id" : 810751,
"num_synth_children" : 371,
"tax_source" : "ncbi:9242,gbif:5289,irmng:104628",
"tree_sources" : [ {
"study_id" : "pg_2853",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "6624"
}, {
"study_id" : "taxonomy",
"git_sha" : "",
"tree_id" : ""
}, {
"study_id" : "pg_420",
"git_sha" : "a2c48df995ddc9fd208986c3d4225112550c8452",
"tree_id" : "522"
} ],
"node_id" : 3021732
}Methods for resolving taxonomic names to Open Tree of Life Taxonomy identifiers (ott ids), including finding synonyms / honomyms and performing fuzzy string matching (for matching misspelled names). These methods can use information about taxonomic context to limit search scope and thereby improve performance (e.g. 'search only plants').
| URL | Verb | Summary |
|---|---|---|
/tnrs/match_names |
POST | Returns a list of potential matches to known taxonomic names. |
/tnrs/autocomplete_name |
POST | Given a partial (from the beginning) to complete taxonomic name, return a list of potential matches. |
/tnrs/contexts |
POST | Return a list of pre-defined taxonomic contexts (i.e. clades), which can be used to limit the scope of tnrs queries. |
/tnrs/infer_context |
POST | Return a taxonomic context given a list of taxonomic names. |
Returns a list of potential matches to known taxonomic names.
POST /tnrs/match_names
Accepts one or more taxonomic names and returns information about potential matches for these names to known taxa in OTT. This service uses taxonomic contexts to disambiguate homonyms and misspelled names; a context may be specified using the context_name parameter. If no context is specified, then the context will be inferred: the shallowest taxonomic context that contains all unambiguous names in the input set will be used. A name is considered unambiguous if it is not a synonym and has only one exact match to any taxon name in the entire taxonomy.
Taxonomic contexts are uncontested higher taxa that have been selected to allow limits to be applied to the scope of TNRS searches (e.g. 'match names only within flowering plants'). Once a context has been identified (either user-specified or inferred), all taxon name matches will performed only against taxa within that context.
For a list of available taxonomic contexts, see the contexts service.
Parameters with bold type definitions are required.
names : strings
An array of taxon names to be queried.
context_name : string
The name of the taxonomic context to be searched
do_approximate_matching : boolean
A boolean indicating whether or not to perform approximate string (a.k.a. "fuzzy") matching. Will greatly improve speed if this is turned OFF (false). By default, however, it is on (true).
ids : strings
An array of ids to use for identifying names. These will be assigned to each name in the names array. If ids is provided, then ids and names must be identical in length.
include_deprecated : boolean
A boolean indicating whether or not to include deprecated taxa in the search.
include_dubious : boolean
Whether to include so-called 'dubious' taxa--those which are not accepted by OTT.
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/tnrs/match_names \
-H "content-type:application/json" -d \
'{"names":["Aster","Symphyotrichum","Erigeron","Barnadesia"]}'Example result:
{
"governing_code" : "ICN",
"unambiguous_name_ids" : [ "Barnadesia", "Erigeron", "Aster", "Symphyotrichum" ],
"unmatched_name_ids" : [ ],
"matched_name_ids" : [ "Barnadesia", "Erigeron", "Aster", "Symphyotrichum" ],
"context" : "Asteraceae",
"includes_deprecated_taxa" : false,
"includes_dubious_names" : false,
"includes_approximate_matches" : true,
"taxonomy" : {
"author" : "open tree of life project",
"weburl" : "https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-Taxonomy",
"source" : "ott2.8"
},
"results" : [ {
"id" : "Barnadesia",
"matches" : [ {
"is_deprecated" : false,
"is_synonym" : false,
"flags" : [ ],
"search_string" : "barnadesia",
"score" : 1.0,
"synonyms" : [ "Barnadesia Mutis", "Barnadesia" ],
"is_approximate_match" : false,
"ot:ottId" : 515698,
"matched_node_id" : 3947526,
"rank" : "",
"matched_name" : "Barnadesia",
"unique_name" : "Barnadesia",
"is_dubious" : false,
"nomenclature_code" : "ICN",
"ot:ottTaxonName" : "Barnadesia"
} ]
}, {
"id" : "Aster",
"matches" : [ {
"is_deprecated" : false,
"is_synonym" : false,
"flags" : [ "EDITED" ],
"search_string" : "aster",
"score" : 1.0,
"synonyms" : [ "Kitamuraea", "Bellidiastrum", "Baccharidiopsis", "Miyamayomena", "Aster", "Heterochaeta", "Crinitaria", "Lasallea", "Conyzanthus", "Linosyris", "Aster L.", "Wardaster", "Borkonstia", "Kitamuraster", "Virgulaster", "Chlamydites", "Weberaster", "Galatella", "Baccharidopsis", "Oreastrum" ],
"is_approximate_match" : false,
"ot:ottId" : 409712,
"matched_node_id" : 3976434,
"rank" : "",
"matched_name" : "Aster",
"unique_name" : "Aster (genus in Australasian lineages)",
"is_dubious" : false,
"nomenclature_code" : "ICN",
"ot:ottTaxonName" : "Aster"
} ]
}, {
"id" : "Erigeron",
"matches" : [ {
"is_deprecated" : false,
"is_synonym" : false,
"flags" : [ "EDITED" ],
"search_string" : "erigeron",
"score" : 1.0,
"synonyms" : [ "Darwiniothamnus", "Stenactis", "Erigeron", "Trimorpha", "fleabanes", "Achaetogeron" ],
"is_approximate_match" : false,
"ot:ottId" : 643717,
"matched_node_id" : 3977809,
"rank" : "",
"matched_name" : "Erigeron",
"unique_name" : "Erigeron",
"is_dubious" : false,
"nomenclature_code" : "ICN",
"ot:ottTaxonName" : "Erigeron"
} ]
}, {
"id" : "Symphyotrichum",
"matches" : [ {
"is_deprecated" : false,
"is_synonym" : false,
"flags" : [ "EDITED" ],
"search_string" : "symphyotrichum",
"score" : 1.0,
"synonyms" : [ "Virgulus", "Symphyotrichum" ],
"is_approximate_match" : false,
"ot:ottId" : 1058735,
"matched_node_id" : 3980020,
"rank" : "",
"matched_name" : "Symphyotrichum",
"unique_name" : "Symphyotrichum",
"is_dubious" : false,
"nomenclature_code" : "ICN",
"ot:ottTaxonName" : "Symphyotrichum"
} ]
} ]
}Given a partial (from the beginning) to complete taxonomic name, return a list of potential matches.
POST /tnrs/autocomplete_name
Assumes the input is a taxon name that may be incomplete (i.e. the beginning of a taxon name such as 'Ast', which would match 'Astelia', 'Astilbe', 'Aster', 'Asteroidea', 'Asteraceae', 'Astrantia', etc.). If the input string is an exact string match to an existing taxon name, then only the exact match will be returned, (i.e. the input 'Aster' will produce a single result 'Aster').
If name expansion identifies a valid genus name, the results will not include species names from within that genus, but if a trailing space exists in the input following a valid genus name, then species names will be returned. For example, both 'Garcin' and 'Garcinia' will match the genus name 'Garcinia' itself but will not match any species names within the genus, but 'Garcinia ' (note the trailing space) will match all the species in the genus, and 'Garcinia m' with match all species names in Garcinia with a specific epithet that starts with 'm'.
IMPORTANT NOTE: This service should not be used for general purpose TNRS queries. It is optimized for and (obviously) intended for use only with autocomplete boxes on web forms. For all name matching purposes other than autocompleting name fields on forms, use the match_names service.
Parameters with bold type definitions are required.
name : string
A string containing a single name (or partial name prefix) to be queried against the db
context_name : string
The name of the taxonomic context to be searched
include_dubious : boolean
A boolean indicating whether or not suppressed taxa should be included in the results. Defaults to false (suppressed taxa are not included).
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/tnrs/autocomplete_name \
-H "content-type:application/json" -d \
'{"name":"Endoxyla","context_name":"All life"}'Example result:
[ {
"ot:ottId" : 4054899,
"unique_name" : "Endoxyla (genus if:1813 in family Boliniaceae)",
"is_dubious" : false,
"is_higher" : true,
"node_id" : 515208
}, {
"ot:ottId" : 1098009,
"unique_name" : "Endoxyla (genus in family Cossidae)",
"is_dubious" : false,
"is_higher" : true,
"node_id" : 2333195
}, {
"ot:ottId" : 429888,
"unique_name" : "Endoxyla (genus ncbi:255778 in family Boliniaceae)",
"is_dubious" : false,
"is_higher" : true,
"node_id" : 515310
} ]Return a list of pre-defined taxonomic contexts (i.e. clades), which can be used to limit the scope of tnrs queries.
POST /tnrs/contexts
Taxonomic contexts are available to limit the scope of TNRS searches. These contexts correspond to uncontested higher taxa such as 'Animals' or 'Land plants'. This service returns a list containing all available taxonomic context names, which may be used as input (via the context_name parameter) to limit the search scope of other services including match_names and autocomplete_name.
Parameters with bold type definitions are required.
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/tnrs/contextsExample result:
{
"FUNGI" : [ "Fungi", "Basidiomycetes", "Ascomycetes" ],
"LIFE" : [ "All life" ],
"ANIMALS" : [ "Animals", "Birds", "Tetrapods", "Mammals", "Amphibians", "Vertebrates", "Arthropods", "Molluscs", "Nematodes", "Platyhelminthes", "Annelids", "Cnidarians", "Arachnides", "Insects" ],
"MICROBES" : [ "Bacteria", "SAR group", "Archaea", "Excavata", "Amoebae", "Centrohelida", "Haptophyta", "Apusozoa", "Diatoms", "Ciliates", "Forams" ],
"PLANTS" : [ "Land plants", "Hornworts", "Mosses", "Liverworts", "Vascular plants", "Club mosses", "Ferns", "Seed plants", "Flowering plants", "Monocots", "Eudicots", "Rosids", "Asterids", "Asterales", "Asteraceae", "Aster", "Symphyotrichum", "Campanulaceae", "Lobelia" ]
}Return a taxonomic context given a list of taxonomic names.
POST /tnrs/infer_context
Find the least inclusive taxonomic context that includes all the unambiguous names in the input set. Unambiguous names are names with exact matches to non-homonym taxa. Ambiguous names (those without exact matches to non-homonym taxa) are indicated in results.
Parameters with bold type definitions are required.
names : strings
An array of taxon names to be queried.
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/tnrs/infer_context \
-H "content-type:application/json" -d \
'{"names":["Pan","Homo","Mus","Bufo","Drosophila"]}'Example result:
{
"context_name" : "Tetrapods",
"context_ott_id" : 229562,
"ambiguous_names" : [ "drosophila" ]
}Methods for accessing information about the current Open Tree of Life taxonomy. These methods require Open Tree of Life Taxonomy identifiers (ott ids), which can be determined using the tnrs to match against taxon names.
| URL | Verb | Summary |
|---|---|---|
/taxonomy/about |
POST | Return information about the taxonomy, including version. |
/taxonomy/lica |
POST | Given a set of ott ids, get the taxon that is the least inclusive common ancestor (the LICA) of all the identified taxa. |
/taxonomy/subtree |
POST | Given an ott id, return complete taxonomy subtree descended from specified taxon. |
/taxonomy/taxon |
POST | Given an ott id, return information about the specified taxon. |
Return information about the taxonomy, including version.
POST /taxonomy/about
Return metadata and information about the taxonomy itself. Currently the available metadata is fairly sparse, but includes (at least) the version, and the location from which the complete taxonomy source files can be downloaded.
Parameters with bold type definitions are required.
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/taxonomy/aboutExample result:
{
"author" : "open tree of life project",
"weburl" : "https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-Taxonomy",
"source" : "ott2.8"
}Given a set of ott ids, get the taxon that is the least inclusive common ancestor (the LICA) of all the identified taxa.
POST /taxonomy/lica
Return information about the least inclusive common ancestral taxon (the LICA) of the identified taxa. A taxonomic LICA is analogous to a most recent common ancestor (MRCA) in a phylogenetic tree. For example, the LICA for the taxa 'Pan' and 'Lemur' in the taxonomy represented by the newick string '(((Pan,Homo,Gorilla)Hominidae,Gibbon)Hominoidea,Lemur)Primates' is 'Primates'.
Parameters with bold type definitions are required.
ott_ids : longs
The ott ids (in an array) for the taxa whose LICA is to be found.
include_lineage : boolean
Whether or not to include information about the higher level taxa that include the identified LICA. By default, this option is set to false. If it is set to true, the lineage will be provided in an ordered array, with the least inclusive taxa at lower indices (i.e. higher indices are higher taxa).
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/taxonomy/lica \
-H 'content-type:application/json' -d \
'{"ott_ids":[515698,590452,409712,643717]}'Example result:
{
"lica" : {
"ot:ottId" : 1042120,
"rank" : "order",
"flags" : [ "SIBLING_LOWER" ],
"unique_name" : "",
"ot:ottTaxonName" : "Asterales",
"synonyms" : [ "Asterales" ],
"node_id" : 3940323
},
"ott_ids_not_found" : [ ]
}Given an ott id, return complete taxonomy subtree descended from specified taxon.
POST /taxonomy/subtree
Extract and return the inclusive taxonomic subtree i.e. (a subset of the taxonomy) below a given taxon. The taxonomy subtree is returned in newick format.
Parameters with bold type definitions are required.
ott_id : long
The OTT id of the taxon of interest.
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/taxonomy/subtree \
-H 'Content-type:application/json' -d '{"ott_id":515698}'Example result:
{
"subtree" : "(Barnadesia_sp._1151,Barnadesia_arborea,Barnadesia_pycnophylla,Barnadesia_polyacantha,Barnadesia_parviflora,Barnadesia_odorata,Barnadesia_glomerata,Barnadesia_dombeyana,(Barnadesia_lehmannii_var._villosa,Barnadesia_lehmannii_var._lehmannii)Barnadesia_lehmannii,Barnadesia_jelskii,Barnadesia_caryophylla,Barnadesia_sp._Palmer_180,Barnadesia_spinosa)Barnadesia"
}Given an ott id, return information about the specified taxon.
POST /taxonomy/taxon
Get information about a known taxon in the taxonomy.
Parameters with bold type definitions are required.
ott_id : long
The OTT id of the taxon of interest.
include_lineage : boolean
Whether or not to include information about all the higher level taxa that include this one. By default, this option is set to false. If it is set to true, the lineage will be provided in an ordered array, with the least inclusive taxa at lower indices (i.e. higher indices are higher taxa).
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/taxonomy/taxon \
-H 'content-type:application/json' -d '{"ott_id":515698}'Example result:
{
"ot:ottId" : 515698,
"rank" : "genus",
"flags" : [ ],
"unique_name" : "",
"synonyms" : [ "Barnadesia", "Barnadesia Mutis" ],
"ot:ottTaxonName" : "Barnadesia",
"node_id" : 3947526
}Source trees are associated with studies (publications), and one study can contain multiple trees. OpenTree uses a Git repository of NexSON files as the central datastore, called phylesystem. Code for an API for the OpenTree treestore is in this Github repository and there is detailed documentation of the datastore API. We also have a study index in neo4j that provides methods that search across studies.
| URL | Verb | Summary |
|---|---|---|
/studies/find_studies |
POST | Return a list of studies that match a given property. If no property provided, returns a list of all studies. |
/studies/find_trees |
POST | Return a list of trees (and the studies that contain them) that match a given property. |
/studies/properties |
POST | Return a list of properties that can be used to search studies and trees. |
/study/{STUDY_ID} |
GET | Return a study. |
/study/{STUDY_ID}/tree/{TREE_ID} |
GET | Return a tree from within a study. |
Return a list of studies that match a given property. If no property provided, returns a list of all studies.
POST /studies/find_studies
Perform a simple search for indexed studies. To find all studies, omit both the property and the value from your query.
Parameters with bold type definitions are required.
exact : boolean
Whether to perform exact matching ONLY. Defaults to false, i.e. fuzzy matching is enabled. Fuzzy matching is only available for some string properties.
property : string
The property to be searched on. A list of searchable properties is available from the properties service. To find all studies, omit both the property and the value from your query.
value : string
The value to be searched. This must be passed as a string, but will be converted to the datatype corresponding to the specified searchable value. To find all studies, omit both the property and the value from your query.
verbose : boolean
Whether or not to include all metadata. By default, only the nexson ids of elements will be returned.
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/studies/find_studies \
-H "content-type:application/json" -d \
'{"property":"ot:studyId","value":"pg_719","verbose":true}'Example result:
{
"matched_studies" : [ ]
}Return a list of trees (and the studies that contain them) that match a given property.
POST /studies/find_trees
Perform a simple search for trees in indexed studies.
Parameters with bold type definitions are required.
property : string
The property to be searched on. A list of searchable properties is available from the properties service.
value : string
The value to be searched. This must be passed as a string, but will be converted to the datatype corresponding to the specified searchable value.
exact : boolean
Whether to perform exact matching ONLY. Defaults to false, i.e. fuzzy matching is enabled. Fuzzy matching is only available for some string properties.
verbose : boolean
Whether or not to include all metadata. By default, only the nexson ids of elements will be returned.
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/studies/find_trees \
-H "content-type:application/json" -d \
'{"property":"ot:ottTaxonName","value":"Garcinia"}'Example result:
{
"matched_studies" : [ {
"matched_trees" : [ {
"nexson_id" : "tree5465",
"oti_tree_id" : "2539_tree5465"
}, {
"nexson_id" : "tree6294",
"oti_tree_id" : "2539_tree6294"
} ],
"ot:studyId" : "2539"
}, {
"matched_trees" : [ {
"nexson_id" : "tree554",
"oti_tree_id" : "438_tree554"
} ],
"ot:studyId" : "438"
}, {
"matched_trees" : [ {
"nexson_id" : "tree46",
"oti_tree_id" : "230_tree46"
}, {
"nexson_id" : "tree5504",
"oti_tree_id" : "230_tree5504"
} ],
"ot:studyId" : "230"
}, {
"matched_trees" : [ {
"nexson_id" : "tree6117",
"oti_tree_id" : "2610_tree6117"
} ],
"ot:studyId" : "2610"
}, {
"matched_trees" : [ {
"nexson_id" : "tree319",
"oti_tree_id" : "187_tree319"
} ],
"ot:studyId" : "187"
}, {
"matched_trees" : [ {
"nexson_id" : "tree1250",
"oti_tree_id" : "137_tree1250"
}, {
"nexson_id" : "tree1251",
"oti_tree_id" : "137_tree1251"
}, {
"nexson_id" : "tree1252",
"oti_tree_id" : "137_tree1252"
} ],
"ot:studyId" : "137"
}, {
"matched_trees" : [ {
"nexson_id" : "tree1396",
"oti_tree_id" : "41_tree1396"
} ],
"ot:studyId" : "41"
}, {
"matched_trees" : [ {
"nexson_id" : "tree5017",
"oti_tree_id" : "271_tree5017"
}, {
"nexson_id" : "tree163",
"oti_tree_id" : "271_tree163"
} ],
"ot:studyId" : "271"
}, {
"matched_trees" : [ {
"nexson_id" : "tree67",
"oti_tree_id" : "232_tree67"
}, {
"nexson_id" : "tree60",
"oti_tree_id" : "232_tree60"
}, {
"nexson_id" : "tree71",
"oti_tree_id" : "232_tree71"
}, {
"nexson_id" : "tree66",
"oti_tree_id" : "232_tree66"
}, {
"nexson_id" : "tree56",
"oti_tree_id" : "232_tree56"
}, {
"nexson_id" : "tree48",
"oti_tree_id" : "232_tree48"
}, {
"nexson_id" : "tree68",
"oti_tree_id" : "232_tree68"
}, {
"nexson_id" : "tree52",
"oti_tree_id" : "232_tree52"
}, {
"nexson_id" : "tree54",
"oti_tree_id" : "232_tree54"
}, {
"nexson_id" : "tree61",
"oti_tree_id" : "232_tree61"
}, {
"nexson_id" : "tree57",
"oti_tree_id" : "232_tree57"
}, {
"nexson_id" : "tree51",
"oti_tree_id" : "232_tree51"
}, {
"nexson_id" : "tree62",
"oti_tree_id" : "232_tree62"
}, {
"nexson_id" : "tree70",
"oti_tree_id" : "232_tree70"
}, {
"nexson_id" : "tree53",
"oti_tree_id" : "232_tree53"
}, {
"nexson_id" : "tree69",
"oti_tree_id" : "232_tree69"
}, {
"nexson_id" : "tree55",
"oti_tree_id" : "232_tree55"
} ],
"ot:studyId" : "232"
}, {
"matched_trees" : [ {
"nexson_id" : "tree6203",
"oti_tree_id" : "2665_tree6203"
} ],
"ot:studyId" : "2665"
}, {
"matched_trees" : [ {
"nexson_id" : "tree43",
"oti_tree_id" : "227_tree43"
} ],
"ot:studyId" : "227"
}, {
"matched_trees" : [ {
"nexson_id" : "tree153",
"oti_tree_id" : "265_tree153"
} ],
"ot:studyId" : "265"
}, {
"matched_trees" : [ {
"nexson_id" : "tree3880",
"oti_tree_id" : "1903_tree3880"
} ],
"ot:studyId" : "1903"
}, {
"matched_trees" : [ {
"nexson_id" : "tree996",
"oti_tree_id" : "71_tree996"
}, {
"nexson_id" : "tree997",
"oti_tree_id" : "71_tree997"
} ],
"ot:studyId" : "71"
}, {
"matched_trees" : [ {
"nexson_id" : "tree5",
"oti_tree_id" : "16_tree5"
} ],
"ot:studyId" : "16"
}, {
"matched_trees" : [ {
"nexson_id" : "tree241",
"oti_tree_id" : "27_tree241"
}, {
"nexson_id" : "tree243",
"oti_tree_id" : "27_tree243"
} ],
"ot:studyId" : "27"
} ]
}Return a list of properties that can be used to search studies and trees.
POST /studies/properties
Get a list of properties that can be used to search for studies and trees.
Parameters with bold type definitions are required.
Example command:
$ curl -X POST http://devapi.opentreeoflife.org/v2/studies/propertiesExample result:
{
"tree_properties" : [ "ot:studyPublicationReference", "is_deprecated", "ot:focalCladeOTTTaxonName", "ot:studyLastEditor", "ot:comment", "ot:studyModified", "ot:studyLabel", "ot:studyId", "ot:dataDeposit", "ot:studyUploaded", "ot:authorContributed", "ot:studyYear", "ot:focalCladeTaxonName", "ot:tag", "ot:curatorName", "ot:studyPublication", "ot:focalCladeOTTId", "ot:focalClade" ],
"study_properties" : [ "ot:studyPublicationReference", "is_deprecated", "ot:focalCladeOTTTaxonName", "ot:studyLastEditor", "ot:comment", "ot:studyModified", "ot:studyLabel", "ot:studyId", "ot:dataDeposit", "ot:studyUploaded", "ot:authorContributed", "ot:studyYear", "ot:focalCladeTaxonName", "ot:tag", "ot:curatorName", "ot:studyPublication", "ot:focalCladeOTTId", "ot:focalClade" ]
}Return a study.
GET /study/{STUDY_ID}
Given a studyID, return a JSON object. The 'data' property of that object will hold the NexSON of that study. More detailed documentation of the possible arguments and return values (including as NeXML, NEXUS, or newick) are at phylesystem-api/docs/README.md
Parameters with bold type definitions are required.
Example command:
$ curl http://devapi.opentreeoflife.org/v2/study/pg_1144Example result:
{"commentHTML": "", "branch2sha": {"master": "89945d5387e50647a6c0e359941a1db9e779e5c8"}, "sha": "89945d5387e50647a6c0e359941a1db9e779e5c8", "duplicateStudyIDs": [], "versionHistory": [{"author_email": "[email protected]", "author_name": "Mark T. Holder", "message_subject": "copied versions from phylesystem-1", "date_ISO_8601": "2014-05-29 12:02:40 -0500", "date": "Thu, 29 May 2014 12:02:40 -0500", "id": "6c86be17db3e238305212c19930f6163b61607a3", "relative_date": "4 months ago"}, {"author_email": "[email protected]", "author_name": "Mark T. Holder", "message_subject": "import from phylografter using migrate_testing_phylesystem", "date_ISO_8601": "2014-03-31 22:12:49 -0500", "date": "Mon, 31 Mar 2014 22:12:49 -0500", "id": "6e1360b70de456f640fa26e6c4405deb83e1a2fc", "relative_date": "6 months ago"}], "data": {"nexml": {"meta": [{"message": [], "@xsi:type": "nex:LiteralMeta", "@property": "ot:messages"}, {"@datatype": "xsd:string", "@property": "ot:studyPublicationReference", "@xsi:type": "nex:LiteralMeta", "$": "Gryganskyi, Andrii P., Richard A. Humber, Matthew E. Smith, Jolanta Miadlikovska, Steven Wu, Kerstin Voigt, Grit Walther, Iryna M. Anishchenko, and Rytas Vilgalys. \"Molecular Phylogeny of the< i> Entomophthoromycota</i>.\" Molecular Phylogenetics and Evolution: Volume 65, Issue 2, November 2012, Pages 682\u2013694"}, {"@datatype": "xsd:string", "@property": "ot:focalCladeOTTTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Entomophthoromycota"}, {"@datatype": "xsd:string", "@property": "ot:curatorName", "@xsi:type": "nex:LiteralMeta", "$": "Romina Gazis"}, {"@datatype": "xsd:int", "@property": "ot:studyYear", "@xsi:type": "nex:LiteralMeta", "$": 2012}, {"@property": "ot:annotationEvents", "@xsi:type": "nex:LiteralMeta", "annotation": [{"@preserve": false, "@description": "Open Tree NexSON validation", "@passedChecks": true, "@about": "#peyotl-validator-event", "@wasAssociatedWithAgentId": "peyotl-validator", "message": [{"@severity": "WARNING", "@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:ottId"], "refersTo": {"@idref": ["otu227255", "otu227259"], "@otuID": ["otu227255", "otu227259"], "@top": "otus", "@otusID": "otus1144"}}, {"@severity": "WARNING", "@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:dataDeposit"], "refersTo": {"@idref": "study", "@top": "nexml"}}, {"@severity": "WARNING", "@code": "MISSING_OPTIONAL_KEY", "data": ["^ot:inGroupClade"], "refersTo": {"@idref": "tree2324", "@treeID": "tree2324", "@treesID": "tree2324", "@top": "trees"}}], "@id": "peyotl-validator-event"}]}, {"@datatype": "xsd:string", "@property": "ot:studyId", "@xsi:type": "nex:LiteralMeta", "$": "1144"}, {"@rel": "ot:studyPublication", "@href": "http://dx.doi.org/10.1016/j.ympev.2012.07.026", "@xsi:type": "nex:ResourceMeta"}, {"@property": "ot:agents", "@xsi:type": "nex:LiteralMeta", "agent": [{"@about": "#peyotl-validator", "@description": "validator of NexSON constraints as well as constraints that would allow a study to be imported into the Open Tree of Life's phylogenetic synthesis tools", "@name": "validate_ot_nexson.py", "@version": "0.0.4a", "@url": "https://github.com/OpenTreeOfLife/peyotl", "invocation": {"otherProperty": [{"name": "pythonVersion", "value": "2.7.5+"}, {"name": "pythonImplementation", "value": "CPython"}], "commandLine": ["--embed", "--agent-only"]}, "@id": "peyotl-validator"}]}, {"@datatype": "xsd:string", "@property": "ot:tag", "@xsi:type": "nex:LiteralMeta", "$": "LSU"}, {"@datatype": "xsd:string", "@property": "ot:tag", "@xsi:type": "nex:LiteralMeta", "$": "ML"}, {"@datatype": "xsd:string", "@property": "ot:tag", "@xsi:type": "nex:LiteralMeta", "$": "SSU"}, {"@datatype": "xsd:int", "@property": "ot:focalClade", "@xsi:type": "nex:LiteralMeta", "$": 97730}], "@xmlns": {"xsd": "http://www.w3.org/2001/XMLSchema#", "ot": "http://purl.org/opentree-terms#", "$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "@id": "study", "@nexml2json": "0.0.0", "@about": "#study", "trees": {"@about": "#trees1144", "tree": [{"node": [{"@about": "#node552029", "@id": "node552029", "@root": true}, {"@otu": "otu227247", "meta": [{"@datatype": "xsd:boolean", "@property": "ot:isLeaf", "@xsi:type": "nex:LiteralMeta", "$": true}], "@id": "node552030", "@about": "#node552030"}, {"@about": "#node552031", "@id": "node552031"}, {"@about": "#node552032", "@id": "node552032"}, {"@about": "#node552033", "@id": "node552033"}, {"@about": "#node552034", "@id": "node552034"}, {"@otu": "otu227248", "meta": [{"@datatype": "xsd:boolean", "@property": "ot:isLeaf", "@xsi:type": "nex:LiteralMeta", "$": true}], "@id": "node552035", "@about": "#node552035"}, {"@otu": "otu227249", "meta": [{"@datatype": "xsd:boolean", "@property": "ot:isLeaf", "@xsi:type": "nex:LiteralMeta", "$": true}], "@id": "node552036", "@about": "#node552036"}, {"@about": "#node552037", "@id": "node552037"}, {"@about": "#node552038", "@id": "node552038"}, {"@otu": "otu227250", "meta": [{"@datatype": "xsd:boolean", "@property": "ot:isLeaf", "@xsi:type": "nex:LiteralMeta", "$": true}], "@id": "node552039", "@about": "#node552039"}, {"@otu": "otu227251", 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"ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Erynia ovispora"}], "@id": "otu227290"}, {"@about": "#otu227291", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 925119}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Conidiobolus thromboides 70 E149"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Conidiobolus thromboides"}], "@id": "otu227291"}, {"@about": "#otu227292", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 178760}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Conidiobolus osmodes 79 E101"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Conidiobolus osmodes"}], "@id": "otu227292"}, {"@about": "#otu227293", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 956401}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Mortierella verticillata 291 Z2"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Mortierella verticillata"}], "@id": "otu227293"}, {"@about": "#otu227294", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 837861}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Endogone pisiformis 539 Z5"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Endogone pisiformis"}], "@id": "otu227294"}, {"@about": "#otu227295", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 199302}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Umbelopsis ramanniana 144 Z7"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Umbelopsis ramanniana"}], "@id": "otu227295"}, {"@about": "#otu227296", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 363292}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Rhizopus stolonifer 632 Z6"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Rhizopus stolonifer"}], "@id": "otu227296"}, {"@about": "#otu227297", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 735973}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Phycomyces blakesleeanus 184 Z8"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Phycomyces blakesleeanus"}], "@id": "otu227297"}, {"@about": "#otu227298", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 837854}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Glomus intraradices 48 Z17"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Rhizophagus intraradices"}], "@id": "otu227298"}, {"@about": "#otu227299", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 41889}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Olpidium brassicae"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Olpidium brassicae"}], "@id": "otu227299"}, {"@about": "#otu227300", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 260279}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Physoderma maydis 19 C3"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Physoderma maydis"}], "@id": "otu227300"}, {"@about": "#otu227301", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 543909}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Synchytrium macrosporum"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Synchytrium macrosporum"}], "@id": "otu227301"}, {"@about": "#otu227302", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 214618}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Karlingiomyces sp"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Karlingiomyces"}], "@id": "otu227302"}, {"@about": "#otu227303", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 737608}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Rhizophydium sp"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Rhizophydium"}], "@id": "otu227303"}, {"@about": "#otu227304", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 858873}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Batrachochytrium dendrobatidis 21 C4"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Batrachochytrium dendrobatidis"}], "@id": "otu227304"}, {"@about": "#otu227305", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 646980}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Rhizoclosmatium sp"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Rhizoclosmatium"}], "@id": "otu227305"}, {"@about": "#otu227306", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 956065}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Polychytrium aggregatum"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Polychytrium aggregatum"}], "@id": "otu227306"}, {"@about": "#otu227307", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 306899}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Gaertneriomyces semiglobiferus"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Gaertneriomyces semiglobifer"}], "@id": "otu227307"}, {"@about": "#otu227308", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 306907}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Powellomyces sp"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Powellomyces"}], "@id": "otu227308"}, {"@about": "#otu227309", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 708156}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Spizellomyces punctatus"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Spizellomyces punctatus"}], "@id": "otu227309"}, {"@about": "#otu227310", "meta": [{"@datatype": "xsd:int", "@property": "ot:ottId", "@xsi:type": "nex:LiteralMeta", "$": 285549}, {"@datatype": "xsd:string", "@property": "ot:originalLabel", "@xsi:type": "nex:LiteralMeta", "$": "Catenomyces sp"}, {"@datatype": "xsd:string", "@property": "ot:ottTaxonName", "@xsi:type": "nex:LiteralMeta", "$": "Catenomyces"}], "@id": "otu227310"}]}, "@version": "0.9"}}}
Return a tree from within a study.
GET /study/{STUDY_ID}/tree/{TREE_ID}
Given a studyID and the ID of one of its trees, return a JSON object for the tree. More detailed documentation of the possible arguments and return values (including as NEXUS or newick) are at phylesystem-api/docs/README.md
Parameters with bold type definitions are required.
Example command:
$ curl http://devapi.opentreeoflife.org/v2/study/pg_1144/tree/tree2324Example result:
{"tree2324": {"^ot:rootNodeId": "node552029", "^ot:curatedType": "ML", "nodeById": {"node552132": {"@otu": "otu227296"}, "node552133": {"@otu": "otu227297"}, "node552130": {"@otu": "otu227295"}, "node552131": {}, "node552136": {"@otu": "otu227299"}, "node552137": {"@otu": "otu227300"}, "node552134": {"@otu": "otu227298"}, "node552135": {}, "node552138": {}, "node552139": {}, "node552147": {"@otu": "otu227305"}, "node552146": {}, "node552145": {}, "node552144": {"@otu": "otu227304"}, "node552143": {"@otu": "otu227303"}, "node552142": {}, "node552141": {"@otu": "otu227302"}, "node552140": {"@otu": "otu227301"}, "node552149": {}, "node552148": {"@otu": "otu227306"}, "node552121": {}, "node552120": {"@otu": "otu227290"}, "node552123": {"@otu": "otu227292"}, "node552122": {"@otu": "otu227291"}, "node552125": {"@otu": "otu227293"}, "node552124": {}, "node552127": {"@otu": "otu227294"}, "node552126": {}, "node552129": {}, "node552108": {}, "node552039": {"@otu": "otu227250"}, "node552038": {}, "node552033": {}, "node552032": {}, "node552031": {}, "node552030": {"@otu": "otu227247"}, "node552037": {}, "node552036": {"@otu": "otu227249"}, "node552035": {"@otu": "otu227248"}, "node552034": {}, "node552114": {"@otu": "otu227286"}, "node552115": {"@otu": "otu227287"}, "node552116": {}, "node552117": {"@otu": "otu227288"}, "node552110": {"@otu": "otu227284"}, "node552111": {}, "node552112": {}, "node552113": {"@otu": "otu227285"}, "node552118": {}, "node552119": {"@otu": "otu227289"}, "node552048": {}, "node552049": {"@otu": "otu227255"}, "node552046": {"@otu": "otu227253"}, "node552047": {"@otu": "otu227254"}, "node552044": {"@otu": "otu227252"}, "node552045": {}, "node552042": {}, "node552043": {}, "node552040": {"@otu": "otu227251"}, "node552041": {}, "node552059": {"@otu": "otu227259"}, "node552058": {}, "node552055": {}, "node552054": {}, "node552057": {"@otu": "otu227258"}, "node552056": {"@otu": "otu227257"}, "node552051": {}, "node552050": {"@otu": "otu227256"}, "node552053": {}, "node552052": {}, "node552062": {"@otu": "otu227261"}, "node552060": {}, "node552061": {"@otu": "otu227260"}, "node552109": {}, "node552063": {}, "node552064": {}, "node552065": {"@otu": "otu227262"}, "node552066": {}, "node552067": {"@otu": "otu227263"}, "node552068": {}, "node552069": {"@otu": "otu227264"}, "node552101": {"@otu": "otu227279"}, "node552100": {}, "node552107": {"@otu": "otu227283"}, "node552106": {"@otu": "otu227282"}, "node552105": {"@otu": "otu227281"}, "node552104": {}, "node552103": {"@otu": "otu227280"}, "node552088": {"@otu": "otu227273"}, "node552089": {"@otu": "otu227274"}, "node552102": {}, "node552082": {"@otu": "otu227269"}, "node552083": {"@otu": "otu227270"}, "node552080": {}, "node552081": {}, "node552086": {"@otu": "otu227272"}, "node552087": {}, "node552084": {}, "node552085": {"@otu": "otu227271"}, "node552077": {}, "node552076": {}, "node552075": {}, "node552074": {"@otu": "otu227267"}, "node552073": {"@otu": "otu227266"}, "node552072": {}, "node552071": {}, "node552070": {"@otu": "otu227265"}, "node552079": {"@otu": "otu227268"}, "node552078": {}, "node552099": {}, "node552098": {}, "node552091": {}, "node552090": {}, "node552093": {"@otu": "otu227275"}, "node552092": {}, "node552095": {"@otu": "otu227276"}, "node552094": {}, "node552097": {"@otu": "otu227278"}, "node552096": {"@otu": "otu227277"}, "node552128": {}, "node552029": {"@root": true}, "node552150": {"@otu": "otu227307"}, "node552151": {}, "node552152": {"@otu": "otu227308"}, "node552153": {"@otu": "otu227309"}, "node552154": {"@otu": "otu227310"}}, "^ot:tag": ["delete me"], "@xsi:type": "nex:FloatTree", "edgeBySourceId": {"node552116": {"edge552118": {"@source": "node552116", "@length": 0.06619625, "@target": "node552118"}, "edge552117": {"@source": "node552116", "@length": 0.07581493, "@target": "node552117"}}, "node552131": {"edge552133": {"@source": "node552131", "@length": 0.11891857, "@target": "node552133"}, "edge552132": {"@source": "node552131", "@length": 0.10472929, "@target": "node552132"}}, "node552111": {"edge552112": {"@source": "node552111", "@length": 0.02843322, "@target": "node552112"}, "edge552115": {"@source": "node552111", "@length": 0.0275771, "@target": "node552115"}}, "node552112": {"edge552113": {"@source": "node552112", "@length": 0.00757353, "@target": "node552113"}, "edge552114": {"@source": "node552112", "@length": 0.00858123, "@target": "node552114"}}, "node552135": {"edge552137": {"@source": "node552135", "@length": 0.22977589, "@target": "node552137"}, "edge552136": {"@source": "node552135", "@length": 0.12247605, "@target": "node552136"}}, "node552138": {"edge552139": {"@source": "node552138", "@length": 0.02394478, "@target": "node552139"}, "edge552142": {"@source": "node552138", "@length": 0.03572564, "@target": "node552142"}}, "node552139": {"edge552140": {"@source": "node552139", "@length": 0.46977686, "@target": "node552140"}, "edge552141": {"@source": "node552139", "@length": 0.20696697, "@target": "node552141"}}, "node552118": {"edge552119": {"@source": "node552118", "@length": 0.01484126, "@target": "node552119"}, "edge552120": {"@source": "node552118", "@length": 0.006078, "@target": "node552120"}}, "node552099": {"edge552107": {"@source": "node552099", "@length": 0.05413815, "@target": "node552107"}, "edge552100": {"@source": "node552099", "@length": 0.01307394, "@target": "node552100"}}, "node552098": {"edge552108": {"@source": "node552098", "@length": 0.00949916, "@target": "node552108"}, "edge552099": {"@source": "node552098", "@length": 0.02662321, "@target": "node552099"}}, "node552072": {"edge552074": {"@source": "node552072", "@length": 0.08210585, "@target": "node552074"}, "edge552073": {"@source": "node552072", "@length": 0.03547935, "@target": "node552073"}}, "node552091": {"edge552097": {"@source": "node552091", "@length": 0.02443536, "@target": "node552097"}, "edge552092": {"@source": "node552091", "@length": 0.03571147, "@target": "node552092"}}, "node552090": {"edge552098": {"@source": "node552090", "@length": 0.01530024, "@target": "node552098"}, "edge552091": {"@source": "node552090", "@length": 0.05775691, "@target": "node552091"}}, "node552092": {"edge552094": {"@source": "node552092", "@length": 0.01674139, "@target": "node552094"}, "edge552093": {"@source": "node552092", "@length": 0.02371265, "@target": "node552093"}}, "node552094": {"edge552096": {"@source": "node552094", "@length": 0.00324711, "@target": "node552096"}, "edge552095": {"@source": "node552094", "@length": 0.00071263, "@target": "node552095"}}, "node552124": {"edge552126": {"@source": "node552124", "@length": 0.02971552, "@target": "node552126"}, "edge552125": {"@source": "node552124", "@length": 0.1487559, "@target": "node552125"}}, "node552146": {"edge552148": {"@source": "node552146", "@length": 0.17327725, "@target": "node552148"}, "edge552147": {"@source": "node552146", "@length": 0.31910682, "@target": "node552147"}}, "node552145": {"edge552149": {"@source": "node552145", "@length": 0.06262751, "@target": "node552149"}, "edge552146": {"@source": "node552145", "@length": 0.39253037, "@target": "node552146"}}, "node552151": {"edge552153": {"@source": "node552151", "@length": 0.06640826, "@target": "node552153"}, "edge552152": {"@source": "node552151", "@length": 0.10865263, "@target": "node552152"}}, "node552060": {"edge552062": {"@source": "node552060", "@length": 0.4091589, "@target": "node552062"}, "edge552061": {"@source": "node552060", "@length": 0.19941555, "@target": "node552061"}}, "node552104": {"edge552105": {"@source": "node552104", "@length": 0.02973593, "@target": "node552105"}, "edge552106": {"@source": "node552104", "@length": 0.01196457, "@target": "node552106"}}, "node552109": {"edge552111": {"@source": "node552109", "@length": 0.0059751, "@target": "node552111"}, "edge552110": {"@source": "node552109", "@length": 0.02590525, "@target": "node552110"}}, "node552063": {"edge552071": {"@source": "node552063", "@length": 0.0931549, "@target": "node552071"}, "edge552064": {"@source": "node552063", "@length": 0.06748044, "@target": "node552064"}}, "node552064": {"edge552066": {"@source": "node552064", "@length": 0.0416101, "@target": "node552066"}, "edge552065": {"@source": "node552064", "@length": 0.15653844, "@target": "node552065"}}, "node552142": {"edge552143": {"@source": "node552142", "@length": 0.13023322, "@target": "node552143"}, "edge552144": {"@source": "node552142", "@length": 0.30290689, "@target": "node552144"}}, "node552066": {"edge552068": {"@source": "node552066", "@length": 0.01002917, "@target": "node552068"}, "edge552067": {"@source": "node552066", "@length": 0.02859576, "@target": "node552067"}}, "node552128": {"edge552129": {"@source": "node552128", "@length": 0.05086973, "@target": "node552129"}, "edge552134": {"@source": "node552128", "@length": 0.32235586, "@target": "node552134"}}, "node552068": {"edge552069": {"@source": "node552068", "@length": 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The following links provide information about ongoing development: methods being tested, developed or discussed.
- documentation of the datastore API
- list of neo4j methods
- Python library for interacting with OpenTree APIs
- Overview of methods used internally between OpenTree components
If you have questions or feedback, leave an issue on GitHub or join us on IRC on the #opentreeoflife channel on Freenode.