Taxon Frameworks

One of the strengths and weaknesses of iNaturalist is that there is a single taxonomy that we all share as we work together to identify observations by hanging them on this tree of life. This means that it’s critical that we understand each other when we refer to branches of the tree. This is becoming more challenging as the iNaturalist community becomes larger and more diverse.

Consider the following example: what do we mean by the Kingdom Protozoa? Before 1969, most people considered there to be just four kingdoms: Plants, Animals, Fungi, and Protozoa. Any living thing that wasn’t a plant, animal, or fungus was considered Protozoa. By the 1980s, organisms without cell nuclei were split out of Protozoa into other kingdoms (e.g. Bacteria) and some organisms like kelp were split into a new kingdom Chromista. Protozoa remains a bit of a grab bag of not closely related organisms (we call this a "non-natural" or "non-monophyletic" group) which has led many to continuing subdividing Protozoa even further.

This is relevant to us because when someone identifies an observation on iNaturalist as Protozoa (or any other taxa) before we can have a discussion about identification, it’s important that we’re all on the same page about what we mean by that taxon. By Protozoa do we mean the mainstream concept for the group, a broader one that includes kelp, or do we mean some modern, even narrower concept that excludes lots of other potential organisms?

To address this, we introduced a new section on the taxon pages called Taxonomy Details which includes information about "what we mean" by a particular taxon. For example, navigate to the taxon page for Kingdom Protozoa and click Taxonomy Details in the Taxonomy tab.

The Taxonomy Details page for Protozoa tells us that this taxon is "Covered by a Taxon Framework for Stateofmatter Life sourced to Catalogue of Life: 2018 Annual Checklist". As explained below, this means that the branch of the iNaturalist taxonomy that includes Protozoa generally follows the Catalogue of Life taxonomy. It also tells us that what iNaturalist means by Protozoa exactly matches what Catalogue of Life means.

The information on the taxonomy details page allows us to be explicit about "what we mean" by Protozoa by deferring a lot of the details to Catalogue of Life. When we say Protozoa on iNaturalist we are referring to a group of 11 Phlya distinct from Chromista and seven other Kingdoms.

Taxon Frameworks and Taxon Framework Relationships

To better understand how the system is managing this information, let’s define some new terms. Taxon Frameworks, like the one covering Kingdom Protozoa are always attached to a single taxon (e.g. Stateofmatter Life) and can have coverage "downstream" over descending taxa (e.g. downstream to rank Phylum and thus covering Kingdom Protozoa). If they have an external source (e.g. Catalogue of Life), there can be Taxon Framework Relationships describing the relationship between the external representation of a taxon or taxa (e.g. Kingdom Protozoa on Catalogue of Life) and the internal representation of the taxon or taxa (e.g. Kingdom Protozoa on iNaturalist).

The Taxonomy Details page for Kingdom Protozoa is displaying a Taxonomic Framework Relationship associated with an upstream Taxon Framework attached to Stateofmatter Life. More details about the Taxon Framework attached to Stateofmatter Life are explained on the Taxonomy Details page for Stateofmatter Life. To navigate here from the taxonomy details page for Kingdom Protozoa, click where it says "taxon framework for Stateofmatter Life".

Taxonomy Details pages contain information about an upstream Taxon Framework covering the taxon (if one exists) and also a Taxon Framework attached directly to the taxon (if one exists). First note that unlike Kingdom Protozoa, this taxon isn’t covered by any upstream Taxon Frameworks (nor could it since Stateofmatter Life is the root of the tree and doesn’t have any ancestors). But Stateofmatter Life does define its own Taxon Framework attached to it (the one that is covering Protozoa). This Taxon Framework is sourced to the Catalogue of Life 2018 Annual Checklist and has downstream coverage to rank Phylum (and thus "covers" Kingdom Protozoa).

Taxon Framework coverage

The coverage of a Taxon Framework includes all of the descendants its taxon (Stateofmatter Life) down to its downstream rank (Phylum). The taxon attached to the Taxon Framework (Stateofmatter Life) is called the root of the covered branch and is not considered covered by the taxon framework attached to it. Taxa at the downstream rank (e.g. phyla) are called ‘tips’ of the covered branch. Taxa between the root and the tips are called ‘internodes’.

One caveat is that any other downstream Taxon Frameworks block the flow of ‘coverage’. For example, if there is a Taxon Framework on Kingdom Animalia, Phylum Arthropoda can’t be covered by the Taxon Framework on Stateofmatter Life. Also be aware that it’s iNaturalist’s convention is to graft Unassigned Taxa (e.g. Class Acantharia) directly to coarser nodes (e.g. Kingdom Protozoa) rather than to placeholder taxa like ‘Phylum Unassigned Protozoa’. Any Unassigned Taxa grafted to internodes are not considered ‘covered’ by the Taxon Framework because their rank is below the extent of the downstream coverage.

In figure below, green taxa are 'covered' by the Taxon Framework attached to Life.

Deviations

Remember that the relationship between the external (Catalogue of Life) and internal (iNaturalist) representation of Protozoa was described as a ‘match’ via a Taxon Framework Relationship. This need not always be the case. Within a Taxon Framework, taxa are considered matches if they have the same name, rank, position, and delineation. Position means that the external taxon’s parent is an ancestor of the local taxon. Rather than match to the external taxon, iNaturalist can deviate through one of the following relationships:

one-to-one (e.g. different name, rank, or position)

alternate position (e.g. same name, rank, different position)

one-to-many

many-to-one

many-to-many

not external (e.g. not in CoL)

not internal (e.g. not in iNat)

Navigate to the taxonomy details page for Kingdom Animalia and note where it counts the number of ‘Deviations’. These are Taxon Framework Relationships with relationships other than ‘match’. Click on the number to explore these deviations in more detail.

Managing Taxon Framework Relationships

Imagine we have an Taxon Framework sourced to an external reference with three external taxa. Meanwhile, there are 5 internal taxa on iNaturalist covered by the Taxon Framework.

The next step is to account for the external taxa by wiring them up to the external taxa with Taxon Framework Relationships. This can be automated to some extent, but to do it correctly, things need to be manually inspected an curated.

If the name, rank, parent name, and parent rank of the internal and external taxa are the same, iNaturalist will consider these a ‘Match’ (actually as long as the external taxon parent is an ancestor of the internal taxon it will count as a match) by creating a Taxon Framework Relationship connecting the taxa. Anything internal taxa covered by the taxon framework without a Taxon Framework Relationship are considered ‘Relationship unknowns’.

Unfortunately, to properly map these taxa, curators need to inspect these relationship unknown taxa and ideally either remove them (via a Taxon Change) or accomodate them with Deviations from the reference. Deviations are Taxon Framework Relationships other than Match. For example, if iNaturalist differs from the reference by splitting T. sierrae off from T. torosa, then a the Match Taxon Framework Relationship of T. torosa is misspecified since these taxa mean different things externally (sensu lato) and internally (sensu stricto). This Taxon Framework Relationship should be modified to include T. sierrae as a ‘one-to-many’. If T. novous is a ‘wholly new taxon’ (i.e. one that doesn’t influence what we mean by sister taxa) that is not in the reference but we wish to include in iNaturalist, then a ‘Not external’ Taxon Framework Relationship should be made. Deviations should include notes describing why the Deviation is necessary including any links to relevant flags.

A well curated Taxon Framework should have all taxa documented through taxon framework relationships, whether they match the external reference or are deviations. That is to say, there should be no internal taxa with unknown relationships.

Complete Taxon Frameworks

If a Taxon Framework contains all the taxa in the clade - i.e. all internal taxa and external taxa are accounted for with Taxon Framework Relationships, then it can be marked as "complete" This displays a note (e.g. “all phyla added to the database”) on the taxonomic tree display on the taxon page taxonomy tab. If the complete Taxon Frameworks coverage extends to species, it displays counts (e.g. "x of y species observed"), and "discoveries" and "wanted" in the Trends tab on downstream taxon pages coarser than rank species. Here’s an example.

Taxon Frameworks without sources

Although it is preferable, Taxon Frameworks don’t have to have external sources. Unsourced Taxon Frameworks may be the only option if there are no external global references for a clade available, or if a taxonomy is just too far from what we want on iNaturalist to practically handle with a small number of deviations. Taxon Frameworks without sources can’t have Taxon Framework Relationships. Here’s an example.

Taxon Curators

If a Taxon Framework has Taxon Curators, then only they can:

1) Edit the name/rank/is_active/position of taxa covered by the Taxon Frameworks

2) Commit Taxon Changes that include covered taxa as inputs

3) Graft to covered taxa with ranks coarser than the downstream coverage rank of the relevant Taxon Framework

The are displayed on the taxonomy details page. Here’s an example.

Taxon Frameworks without downstream coverage

It’s also possible to have a Taxon Framework that doesn’t cover any descendants. Such taxon frameworks can’t have taxon curators or be complete but they still allow taxon framework notes to be displayed on the taxonomy details page. Here’s an example.

Revised on March 29, 2019 17:14 by bouteloua bouteloua