ToL Web Services

Downloading the ToL Tree Structure

The tree structure of the Tree of Life web project is available to the public for non-commercial use. You can download either the entire tree or particular branches. Before using this service, please see the Disclaimer and Terms of Use.

Tree Structure Service

URL

The tree structure service url is

http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id=yyy

where yyy is the unique identifier for a group in the ToL database.

Parameters

Most users of the tree structure service need only concern themselves with a single numeric parameter, node_id, which is the unique identifier for a group in the ToL database. In order to download the structure for the entire tree use node_id=1, which is the node id for Life on Earth. The ids of other named nodes may be obtained via the ToL Group ID Service (see above). If a named node also has a ToL branch or leaf page attached to it, you can also get its id from the page url. In ToL page urls, the node id will usually be appended at then end, separated by a slash from the group name. For example, the url for the Bembidion page is:

http://tolweb.org/Bembidion/194

and the id for the Bembidion node is 194.

There is another parameter, optype that can be used to render the output into a different format. Currently a value of 0 (the default) outputs the tree according to the proprietary ToL Response Format. A value of 1 will output the tree in TreeML, a format used for Graph visualization programs.

ToL Response Format

The structure of the tree is contained in a single XML element, the <TREE> element. The <TREE> element contains a single element, <NODE>, which contains zero or more <NODES> elements. This pattern repeats itself out to the tips of the current tree structure of the ToL web project. While the current tree structure is by no means complete, it does extend the actual leaves of the tree (species, subspecies, populations, or strains) in some branches. This is denoted by a special LEAF attribute on NODE elements. Below is a summary of other elements and attributes that are included in the XML file.

NODE Elements Summary

NAME	The official name for the node in the Tree of Life Web Project. Usually, but not always, the valid scientific name for the group.
DESCRIPTION	Brief description of the group.
AUTHORITY	Authors for a given name.
NAMECOMMENT	Additional comments about the node name
COMBINATION_AUTHOR	Names of authors of a new combination.
AUTHDATE	Publication date of the node name.
OTHERNAMES	Element nesting other names that are applied to the entire group represented by the current node.
OTHERNAME	Another names for the entire group, e. g., synonyms, English names, names in other languages, names indicating different taxonomic ranks.
COMMENTS	Comments about another name.
NODES	Children nodes for the current node.

NODE Attributes Summary

EXTINCT	0 - node is not extinct 2 - node is extinct
ID	The unique identifier for the node on the Tree of Life Web Project
CONFIDENCE	Confidence of placement in the tree structure: 0 - confident 1 - incertae sedis in putative position 2 - incertae sedis position unspecified (no putative position in parent group)
PHYLESIS	0 - monophyletic 1 - monophyly uncertain 2 - not monophyletic
LEAF	1 - the node represents a leaf in the Tree of Life (may be applied to species, subspecies, populations, strains) 0 - the node does not represent a leaf (it has or will have descendent nodes on the Tree of Life)
HASPAGE	1 - the node has a page on the Tree of Life Web Project 0 - it doesn't
ITALICIZENAME	1 - the node name should be printed in italics 0 - it should not be printed in italics
INCOMPLETESUBGROUPS	1 - the immediate descendents of the current node do not represent all known subgroups 0 - all immediate subgroups are represented (although they may not all be fleshed out to the leaves of the tree)
SHOWAUTHORITY	1 - show authority data on the ToL web page for this group 0 - don't show authority data
SHOWAUTHORITYCONTAINING	1 - show authority data on the tree/list of the ToL web page for the containing group 0 - don't show authority data
IS_NEW_COMBINATION	1 - the node name is a new combination 0 - it's not a new combination
COMBINATION_DATE	Publication date of the new combination
CHILDCOUNT	Number of descendent nodes.

OTHERNAME Attributes Summary

ISIMPORTANT	1 - important other name: use as subtitle on ToL web pages 0 - not an important other name
ISPREFERRED	1 - preferred other name: use as supertitle on ToL web pages 0 - not a preferred other name
SEQUENCE	Position of the current name in the other names sequence. Determines the sequence in which names are printed on ToL pages.
DATE	Publication date of the other name.
ITALICIZENAME	1 - the other name should be printed in italics 0 - it should not be printed in italics

Disclaimer

Note that the ToL tree structure is still far from complete. Many important groups are missing, and not all branches have undergone expert review. Our ideas about the phylogenetic relationships of organisms are constantly evolving, as more data become available and new analyses are published. The ToL structure will thus be subject to continuous revision and expansion. In its current, incomplete state, the phylogenetic information compiled by ToL contributors is valuable as a preliminary, synthetic estimate of the relationships among a large subset of known organisms.

Terms of Use

The downloadable version of the ToL tree structure is licensed under the Attribution-NonCommercial Creative Commons License. This license applies only to the downloadable XML files containing the ToL tree structure. For the terms and conditions of use of other ToL materials, please refer to the page about Tree of Life Copyright Policies.