Downloading the ToL Tree Structure
Downloading a ToL branch is a two-step process:
- Find the unique ToL identifier for the root node of the branch you want to download:
- Use the ToL Group ID Service to get the NODE ID for a given taxon name.
- Use the ToL Tree Structure Service, which returns the tree structure along with group names and properties of groups.
Tree Structure Service
The tree structure service url is
where yyy is the unique identifier for a group in the ToL database.
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:
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
|ID||The unique identifier for the node on the Tree of Life Web Project|
|CONFIDENCE||Confidence of placement in the tree structure:
|COMBINATION_DATE||Publication date of the new combination|
|CHILDCOUNT||Number of descendent nodes.|
OTHERNAME Attributes Summary
|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.|
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.
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.