How to work with Taxon Framework Relationships

If a Taxon Framework has a source and covers downstream taxa, then it can have Taxon Framework Relationships. These taxon framework relationships are created and edited by iNat curators and describe the mapping between internal taxa on iNaturalist and the external taxa in the reference.

How to set them up


Suppose our external reference had 4 species (Species A, B, C, & E) and internal to iNaturalist we had 4 species (Species B, C, D & E). Without any additional information, iNaturalist will naively map these two sets of species as follows. Species with the same name, rank, and parent will 'match'. Whereas species in one but not both of the sets will be described with 'not internal' or 'not external' relationships. Relationships other than 'match' are collectively known as 'deviations'

The problem is that true 'not external or 'not internal' deviations are actually quite rare. One-to-one, Many-to-one, and One-to-many deviations are much more common (e.g. splitting a ssp off as a species in the external reference would be a 'many-to-one'). But for iNaturalist to understand these more complex mappings, taxon curators need to provide them.

This is done by creating and editing Taxon Framework Relationships. For example, search for Taxon Framework Relationships with relationship 'not internal' associated with the Rodentia Taxon Framework. At the time of this writing, there is a 'not internal' Taxon Framework Relationship linked to the external taxon Marmota kastschenkoi.

A little research reveals that Marmota kastschenkoi was previously considered a subspecies Marmota baibacina kastschenkoi and comprises the northern populations of Marmota baibacina 'sensu lato' (ie 'in the broad sense') .

Its clear that by Marmota baibacina, iNaturalist intends to means this broader 'sensu lato' concept that includes M. kastschenkoi. This is evident by inspecting the distribution (e.g. observations, taxon range map, atlas etc.) and also the taxonomy itself (e.g. Marmota baibacina kastschenkoi exists as a ssp of Marmota baibacina). This means that both the 'not internal' Taxon Framework Relationship for Marmota kastschenkoi and also the 'match' Taxon Framework Relationship for Marmota baibacina (since one is 'sensu lato' and one is in the narrow sense: 'sensu stricto' ) are misspecified.

The former should be deleted, and the latter should be expanded from a 'match' to a 'many to one' by editing the Taxon Framework Relationship and adding Marmota kastschenkoi as an additional 'external taxon'

There are cases when 'not internal' and 'not external' deviations are legitimate. They are used for obscure nodes (e.g. tribes) or ranks (e.g. hybrids) that might be missing from either iNaturalist or the external sources by design. But they also should be used for species 'wholly new to science'.

For example Svensson et al., 2013 describe a new galago from Angola. This species is sympatric with its closest relatives (G. thomasi and G. demidovii) and is much larger. This distinction between "a change in views of what a species is, that is, dependent on which species concept is adopted" and species "wholly new to science" is often blurry. When its not a clearcut case of the former, discerning when it is indeed the latter from the literature can be aggravating. This is made worse by the fact that journal articles tend to try to hype the 'new species discovery' parts of their paper for greater impact even if they are just reshuffling species. There's some nice text on the distinction in Svensson et al., 2013:

"Most new primate species recognized in the 21st century are the result of the taxonomic elevation of previously known subspecies to species (Groves, 2001; Macaca spp.: Kitchener & Groves, 2002; Aotus spp.: Defler & Bueno, 2007; Nomascus spp.: Thinh, Mootnick, Thanh, Nadler, & Roos, 2010; Microcebus spp.: Hotaling et al., 2016). Taxa wholly new to science, however, are also being described (e.g., Rungwecebus kipunji: Davenport et al., 2006; Jones et al., 2005; Tarsius tumpara: Shekelle, Groves, Merker, & Supriatna, 2008; Rhinopithecus strykeri: Geissmann et al., 2010; Nycticebus kayan: Munds et al., 2013)." Legitamite 'non-internal' Taxon Framework Relationships should include information on why the taxon is 'wholly new' and doesn't risk impacting neighbors (e.g. for Galagoides kumbirensis)

For iNaturalist's purposes. this distinction is important to the extent that we can:
1) avoid changes in the interpretation of past identifications
2) avoid associated meta-data with taxa (distribution information, default taxon photos, names etc.) from becoming misspecified

For example, in the Marmota kastschenkoi case, if we failed to alter the Taxon Relationship Framework mapping from 'non internal' to a 'many-to-one' relationship involving Marmota baibacina, then the proper coarse of action for adding Marmota kastschenkoi would be to create a new taxon. This would mean that the existing taxon range and atlas for Marmota baibacina would become misspecified (since they would continue being 'sensu lato' but the existence of Marmota kastschenkoi as a sibling would change the interpretation to 'sensu stricto'). Similarly, existing identifications of Marmota baibacina - which were intended to be interpreted as Marmota baibacina 'sensu lato' would start being interpreted as Marmota baibacina 'sensu stricto' and would result in the appearance of disagreements where none exist.

In contrast, by properly mapping Marmota kastschenkoi with a 'many-to-one' this would indicate that Marmota kastschenkoi should be added through a split and that additional work will be required to properly curate the distribution, identifications and explain to the community what the change means.

In the galago case, the new galago Galagoides kumbirensis can be simply added without any adverse impacts on its relatives.

Who can edit them?


Any taxon that is covered by a sourced Taxon Framework should have a Taxon Framework Relationship. Only curators can create, edit, or destroy Taxon Framework Relationships. If the Taxon Framework has Taxon Curators, only these taxon curators can create, edit or destroy them.

Good housekeeping of Taxon Framework Relationships


Generally, sourced Taxon Frameworks are initially populated through the back end of iNaturalist via a script that reads in the external taxa from the external reference and compares them to the internal iNaturalist taxa covered by the framework. The purpose of the script is to determine which species in iNaturalist aren't in the external reference (and vice versa) once all the deviations are taken into account. The script makes use of the Taxon Framework Relationships to do the mapping and will fail if there are issues with the Taxon Framework Relationships. Therefore its very important that curators take care when creating/editing/destroying Taxon Framework Relationships. Please do not leave loose ends around. For example, in curating Marmota kastschenkoi so that it is mapped through a many-to-one rather than a 'not internal' you need to do two steps (1) delete the 'not internal' Taxon Framework Relationship involving Marmota kastschenkoi and (2) edit the 'match' Taxon Framework Relationship involving Marmota baibacina by adding Marmota kastschenkoi to make it a 'many-to-one'. Just doing one of these two steps will corrupt the Taxon Framework Relationships.

Likewise, if you were to split Marmota baibacina (sensu lato) into Marmota baibacina (sensu stricto) and Marmota kastschenkoi, once the split is committed, remember your work is not done until you remove the many-to-one Taxon Framework Relationship on the inactive Marmota baibacina (sensu lato) and add new 'match' Taxon Framework Relationships to the outputs Marmota kastschenkoi and Marmota baibacina (sensu stricto).

Publicado por loarie loarie, 29 de enero de 2019

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