Improvements to taxonomic curation on iNat - wiki

General :microbe:

  • Recruit more active curators (see backlog of taxon flags)
  • Improve the Curator Guide by making it more user-friendly. Separate “policies” from “how-tos”?
  • Develop a better location to discuss taxonomy than iNaturalist Working Group collection projects (see discussion)

Taxa :hibiscus:

  • Search for inactive taxa in main search (see feature request)
  • Mark a higher taxon as “complete”, e.g. for large plant genera and plant families
  • Indicate which date a clade was considered “complete”
  • Fix incorrect capitalization of names (see feature request)
  • Standarize formatting for hybrids per ICN & ICZN
  • Fix/Standardize incorrect formatting for subgenera, sections, and subsections per ICN & CZN
  • Prevent addition of improperly formatted names from external sources (see bug report)
  • Allow more users to edit taxa at rank=order and above to help clean up backlog of stranded / duplicate taxa
  • Allow more users to edit taxon names to reduce “pointless” taxon changes for things like typing/spelling mistakes, e.g. epithet ending in “-a” vs. “-us” or hybrid symbol “x” -> “×”
  • Fix whatever is broken in the CoL/EoL external lookup tool which all users can use for species creation that is causing so many ungrafted taxa to be created
  • Add a lookup when using the CoL/EoL import tool to see if the name is in the database as a synonym, and if so prompt the user to this effect and ask them if they wish to continue or simply implement the synonym status
  • Identify and lock homonym genera, e.g. so that fish species don’t get automatically grafted to fungi genera

Taxon Pages :mosquito:

  • Clearly visually indicate type of taxon framework relationship, e.g. a color for match vs. deviation vs. unknown and type: alternate position, many-to-one, etc. (see feature request)
  • [+] to view descendants rather than have to click through
  • Automatically incorporate links to external sites like POWO or Reptile Database via Wikidata, like the taxonbar on Wikipedia pages
  • Distinguish between a genus known to be unplaced to subfamily, tribe, or subtribe (no curation action needed) or if the genus was grafted there without checking. Same with species and subgenera and sections
  • FEATURE ADDED Link to edit a taxon included on the taxonomy tree on the Taxonomy tab (see feature request)

Taxon Changes :cricket:

  • Require a source and/or reason for each taxon change (see feature request)
  • Rename “taxon swap” to something more explanatory, i.e. to indicate that it’s a 1:1 name transfer
  • More obvious visual cue that a taxon is flagged on the taxon change draft / final page
  • Generate and commit automatic species and infra-specific taxon swaps when a genus is demoted to a subgenus, a subgenus is promoted to a genus, or a subgenus is moved from one genus to another – and the binomials of the species have to change. Automatically create new taxa for the new binomials and trinomials with the capability to manually edit them if needed (e.g., change the gender suffix).
  • Validate taxon change commit attempts for cases such as:
    • disagreement with existing Taxon Framework Relationship. For changes that would inactivate taxa with “match” TFRs, modify a “deviation” TFR, or activate a missing TFR, at least pop up a caution/confirmation message, and consider requiring “senior curator” approval to complete the commit.
    • high numbers of existing IDs
    • commit attempt by someone other than taxon change author

Taxon Framework Relationships :shell:

  • When new taxa are added, automatically create taxon framework relationship for matches
  • Allow curators to run job to sync from external authorities to create taxon framework relationships rather than require them to be created one by one manually

Taxon Curators :snail:

  • Create personal landing page that lists all flags relevant to the taxa you are curating
  • Add notification for new flags on taxa you are curating (?)
  • Make process to become a taxon curator more transparent
  • Recruit more active taxon curators

Sources :ear_of_rice:

  • Clean up duplicate sources / make taxonomic authorities easier to select
  • Require a source when adding a new taxon

Policies :butterfly:

  • What to do for dang Lepidoptera epithets supposedly “in apposition”?
  • What to do with undescribed species, esp. those that are included in the external authorities? (see discussion)
  • General guidelines regarding when to make changes to align with authority and when to first initiate a discussion to consider community buy-in or potential deviation

This list of ideas is intended to *exclude* things like default photos, conservation statuses, geoprivacy, ranges, checklists, and atlases and just focus on the names / taxonomy.

It’s a wiki, so please edit this post directly. :pencil2:

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Maybe good to have that ability (like Move children to output? currently), but need to verify new binomials (and any consequent trinomials) actually exist first, and will have correct gender terminations. Not sure subgeneric epithets always have to agree with the gender of their parent genus, or vice versa.

(BTW @bouteloua I like your little topic decorations :smile:)

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Note this could be resolved by the point about allowing more options to simply edit the names of taxa that is raised. Thus run the change, then if needed just edit any names to reflect proper gender. It would certainly be faster than doing them all individually.

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Agreed, though I have to say that the current inability to edit taxon names has probably helped to prevent use of that ability to make substantive taxonomic changes. No matter how many times we say that editing a name should only be to correct a spelling error, someone will inevitably not get the memo, and try to make a taxon swap that way. Don’t know that there is any reliable way to code things to allow one but not the other.

Yeah, which is why I didn’t indicate all curators should be allowed to do this. This would tie into the idea to have a curator level for those with a greater amount of experience using the platform.

3 Likes

I would love to be a more active curator on the taxonomy side. I was starting to get the hang of things before we moved to taxon framework relationships and taxon curators. Now, I’ve tried reading the documentation and asking questions, but I still don’t quite understand what I am able to do. I want to help but feel like my hands are tied. So, a number of these improvements would be massively helpful for me. Thanks, @bouteloua!

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@tigerbb You are not alone, and you might find this ongoing discussion of interest too.

Just a note that GBIF has just implemented using the Wikidata taxon links as a standard part of their page for taxa, so if on a Wikidata page the iNaturalist ID is filled in, there will be a direct link from GBIF back to iNaturalist.

2 Likes

@treichard: Generate and commit automatic species taxon swaps when a genus is demoted to a subgenus or a subgenus is promoted to a genus, and the binomials of the species have to change.

Maybe good to have that ability (like Move children to output? currently), but need to verify new binomials (and any consequent trinomials) actually exist first , and will have correct gender terminations. Not sure subgeneric epithets always have to agree with the gender of their parent genus, or vice versa.

Good point. The missing taxa should also be automatically created so that the taxon swaps can be done automatically. And any ranks lower than species also need to be updated similarly. Another case is moving a subgenus from one genus to another.

At the genus and subgenus ranks, there are so many species that the simplest of changes can trigger hours of repetitive work with the current “let’s update just one taxon at a time” philosophy. This is an area where some automation is needed. My current workaround is to make the genus <–> subgenus change, and instead of updating binomials and trinomials, I just make a flag and hope the work would be crowdsourced in the near future. If the work could be automated instead, then the time when binomials don’t match their parent genus would be greatly reduced.

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How would you suggest automating when a change in gender termination of epithets is involved? Seems like that would be some pretty hairy computer code, and still probably wouldn’t catch every nuance.

[EDIT: ok, I saw your wiki edit suggesting ability to manually edit gender changes. I agree, that’s probably the most practical solution. Maybe the system can limit name edits to the last 4 or 5 bytes of the name, to prevent editing entire names to create de-facto taxon changes?]

@jdmore Yes, with your edit, I think we’re on the same page. I would argue for this workflow:

  1. Curator manually creates a genus/subgenus taxon change.
  2. When that change is committed, all the new species/infraspecies taxa with the new genus in the bi/trinomial would be created, and all species/infraspecies taxon swaps would be automatically created and committed.
  3. Curator manually edits the new bi/trinomials to fix gender endings in some fast and easy way without having to slog through creating/committing taxon swaps one at a time.

Maybe it goes without saying, but the workflow also needs to emphasize the

We don’t want to be populating iNaturalist with a bunch of unpublished name combinations.

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I’m likely not understanding the issue, but if two taxon names are both in use, with observations in each, and one of the taxa is misspelled - e.g. has the incorrect epithet ending - wouldn’t a taxon swap be necessary to shift the obs to the correct taxon and make the other inactive?

Or is this simply about 1 taxon which is misspelled?

Thanks for any enlightenment.

What is the issue that requires something to be done? Other than following official published material, checklists, etc.?

1 Like

Correct, and sorry I wasn’t clearer about my scenario. I was getting at the potential for making a complete name change on a single existing taxon, beyond just a spelling correction. We would always want to do that by creating a new taxon and then swapping, not by editing the name of the existing taxon. The issue is how to allow simple spelling corrections while not allowing more substantive name edits.

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Couple issues here. Sometimes the “taxonomic authorities” in the Curator Guide have the spelling or Latin ending incorrect. I’ve sent many errata in to be corrected at Plants of the World Online. When the name is corrected after a change was made on iNat, there then needs to be another taxon change which results in many messy IDs on each observation. I’ve seen iNat curators who are also BugGuide editors go in to change BugGuide immediately after they saw a taxon change on iNat, then make a new taxon change to match BugGuide.

For leps, most species and places have no agreed upon taxonomic authority on iNat anyway. The names used in different checklists vary. How then to determine who’s right? Follow ICZN or which checklist?

My main issues are time spent trying to figure out who’s correct, the unnecessary taxon changes, and all the messy IDs back and forth, and that this is all done to swap a couple letters around at the end of a name, not to indicate any real change to our understanding of the species. I personally mostly avoid curation of this branch because of this issue.

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I don’t know which BugGuide editors are unilaterally making changes to which groups - there are supposed to be discussions on the BugGuide editor forums to determine acceptance of a change or newly described species, and where it fits in the taxonomic tree. Sounds like a dubious practice that circumvents how BugGuide, in collaboration with other editors, determines its taxonomy.

I can’t speak to plants or other insect groups, but I’ll try to explain leps which is handled differently than most-many-all other insect groups.

Most of the world’s lepidopterists some years ago (in the 1990s I believe) decided, either formally or informally, to ignore the ICZN rule concerning gender agreement with a genus change; that is, the epithet remains the same regardless of the new genus’ alleged gender. For newly described leps all ICZN rules are followed and the peer-reviewed publication is the “authority” for the binomial (whether or not an iNat curator believes it’s “incorrectly” formatted). Both genus changes and newly described species wend their weary way to global and regional checklists, iNat, BugGuide, etc. That may take up to 5 years; I can understand why some iNatters hyperventilate over the time lag but that’s only, IMO, because we in the digital age expect instantaneous updates and instantaneous gratification.

Canada and USA: BugGuide is the approved authority for North America north of Mexico insects. It follows the previously mentioned disregard for gender agreement on genus changes for leps. Lep editors follow Pelham (I think) for Papilionoidea. For moths BugGuide revisions come via Moth Photographers Group in concert with the various official North American checklist authors and Wedge MONA Fascicles.

Other Countries or Regions: A list of the global and regional lep checklists and whether gender agreement is followed is on the page 2 table in this paper: Stability in Lepidoptera names is not served by reversal to gender agreement: a response to Wiemers et al. (2018): https://nl.pensoft.net/article/34187/?fbclid=IwAR1sdp3K76hblAXG_Bc7O0TF2vC3k0QmylqAHoepdzhZjiim_GadMlPsWcc

At the end of that paper, under References, is the complete listing of the various checklists for the world.

And that’s why most lepidopterists agreed with you and decided on a different path…