Phylogeny Standard
A phylogeny depicts parent-child relationships of taxa over the course of evolution. Phylogenies can be constructed for any taxonomic unit of organization (e.g., individuals, genotypes, phenotypes, etc.). We use the term taxa to refer generally to entities in a phylogeny.
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Properties
Required Properties
These are the minimum set of properties (i.e., fields) required to specify a phylogeny. You must have this information to conform to the standard.
- id: A unique identifier. Must be a non-negative integer.
- There is a proposal to change this property name: https://github.com/alife-data-standards/alife-data-standards/issues/16
- ancestor_list: A list of ids. These must correspond to other entities (entries) in the current file. They are assumed to refer to the most direct ancestor(s) of this entity that exist with in a file. In many cases, these will be the direct parent(s) of this entity, but this will not always be the case.
Conventional Properties
These are common, but not required properties, for describing phylogenies. If you have any of this information in your data, you should format it conventionally.
- origin_time: Time that this entity first came into existence (in whatever time units the system that generated this data uses).
- destruction_time: Time that this entry went out of existence (in whatever time units the system that generates this data uses).
Extra Properties
Additional properties can always be added (as long as their names do not conflict with the names of existing properties). Some tools may require specific additional properties to be present. If it becomes apparent at any point that one of these properties is of use to a sizable portion of the community, a discussion should be opened about adding it to the official list of conventional properties.
Example
Below is a toy phylogenetic tree and a standard-compliant data table that specifies the phylogeny, including required, conventional, and extra properties.
Suggestions/Issues/Contributions
The phylogeny standard is still under active discussion. Join in here!