Taxonomic backbones for Europe (plus some others...)

Hi everyone! Over the last months, a recurring theme has been the adoption of external taxonomic authorities for the European (= West Palaearctic) region.

This post is meant as an open discussion forum for the – mostly European – iNat community to come up with a set of taxonomic authorities suited for the region, which could then go into the relevant section of the Curator Guide.

@kueda @loarie let us know if there are certain requirements that an external authority should, or has to, fulfil.

So here's my initial suggestion open for discussion:

Plants of Europe: the Euro+Med PlantBase (where treatment is complete), otherwise falling back to the PlantList.

European animals not covered by taxon-specific global lists (eg birds, amphibians, reptiles, spiders...): Fauna Europaea

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In addition to the question of taxonomic authorities with a European focus, I'm also adding a bunch of suggestions for other regions and / or taxa:

Plants of Africa + Madagascar: African Plant Database

Lepidoptera (only moths, and excluding butterflies) of Africa: AfroMoth

Global Orthoptera list: Orthoptera Species File

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I'm tagging a bunch of users into this post who I think might be interested and hope this doesn't feel like spam. If you don't want to follow this discussion, I think you should be able to unsubscribe from this post.

@alvarosaurus @amc @annemirdl @blue_celery @borisb @claudioflamigni @damighez @danieleseglie @deboas @dhobern @dinobiancolini @duarte @enricoschifani @erwin_pteridophilos @fabienpiednoir @fausto @finrod @jasonrgrant @jujurenoult @lancillotto @ldacosta @leo_dapporto @manval @marcello @marcoschmidtffm @martinbishop @mattiamenchetti @purperlibel @qgroom @rmedina @sindic @smuele @tiggrx @torsten @treegrow @vilseskog @wouterkoch @wouterteunissen

Posted by jakob jakob, June 01, 2017 17:23

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The essential requirement is that iNat users and the broader community of people interested in these groups can agree to abide by the decisions of the authority. Beyond that, my main nice-to-have is that the authority has stable URLs for names and preferably concepts, especially when a name is no longer current, e.g. http://marinespecies.org/aphia.php?p=taxdetails&id=718751. I also like to see some citation or explanation of why changes occurred, though in my experience very few taxonomy sites do this (The Jepson Manual in California does a bit, and I try to do it when I make taxon changes that affect a lot of people, e.g. https://www.inaturalist.org/taxon_changes/19503).

Posted by kueda over 2 years ago (Flag)
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What would happen with the many species that occur in more than one region? If, for example, the taxonomic authority used in the US uses one name and the authority used in Europe uses another then which name would be used?

Posted by tiggrx over 2 years ago (Flag)
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Hi, thanks for starting the discussion.

I mailed the GBIF helpdesk to ask them how they do it (I made it very clear that I'm a volunteer at iNat, not one of the crew). This is their answer:

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From: GBIF Helpdesk

The GBIF Backbone taxonomy is refreshed approximately every 3-6 months, and built using the Catalogue of Life, nomenclature data and other available checklists algorithmically.
We then deploy that exposed through an API which is documented here: http://www.gbif.org/developer/species

TNRS mean different things to different people, but I assume you are looking for a service along the lines of “what would name X be according to the GBI taxonomy”. That is what we refer to as the “species match” service which is documented on the API page. An example call would be (here I am deliberately passing in a generic homonym): http://api.gbif.org/v1/species/match?verbose=true&kingdom=Plantae&name=Oenante
(I use the verbose=true flag to show the Animals which come back with very low confidence match)

The more information you pass the higher the confidence in a response: http://api.gbif.org/v1/species/match?verbose=true&kingdom=Plantae&Phylum=Tracheophyta&family=Apiaceae&name=Oenante

I hope this helps and I’ve CC’ed Markus Döring who leads this work and is also situated in Berlin. I am sure he’d be happy to discuss any aspect of this with you directly – we are big fans of the iNaturalist project in the development group.

==================================================

From: Markus Döring (GBIF)

our upcoming portal also has a batch UI tool build on top of our species match API to reconcile name lists:
https://demo.gbif.org/tools/species-lookup

The matching implementation is our own work refined over the years to strike the balance of fuzzy and false matches.
We allow two matching modes, strict and fuzzy. We use fuzzy for occurrence names which are often of varying quality, but strict for authorative taxonomic lists. The strict mode makes use of a names authorship a lot more.

Happy to answer more details.
The code is here just on case:
https://github.com/gbif/checklistbank/blob/master/checklistbank-nub/src/main/java/org/gbif/nub/lookup/fuzzy/NubMatchingServiceImpl.java#L123

Posted by alvarosaurus over 2 years ago (Flag)
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I actually like the GBIF backbone a lot, but my suspicion is that a lot of people will find it unsatisfying for many groups (e.g. fungi). @tiggrx, regarding conflict, we usually attempt some form of triage, e.g. if one authority uses one name but the rest all use another, we might side with the majority. If we have a global authority, we usually side with that over regional ones, though that often causes problems b/c global authorities tend to be way less up-to-date than regional ones. I wish there was a more algorithmic approach, but short of some global governing body of taxonomy that everyone acknowledges and respects, I think the best anyone can do is follow the heuristics of being as current as possible while doing the least harm (e.g. excessive taxonomic churn to the point that no one knows what any names mean any more).

Posted by kueda over 2 years ago (Flag)
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@markus Döring is on iNat

Posted by jakob over 2 years ago (Flag)
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Concerning plants in Europe and Africa, I would agree with Jakobs suggestions (Euro+Med, African Plants Database), especially since TPL is no longer updated to a new version (at least that's my latest infos) and it is unclear which +/- global database may best play that role in the near future (Tropicos, POWO?). The sometimes confusing "accepted for S Africa, rejected for Tropical Africa" will be resolved in APD soon.

Posted by marcoschmidtffm over 2 years ago (Flag)
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Thanks to jakob for starting this discussion. Problems can arise even with the Plant List.
I think it is important to have a clear exposition of the issues rather than have a single final "right answer".
A case you might like consider is http://www.inaturalist.org/observations/1336290

I am not sure if there are many problems with Palæarctic/Nearctic taxa?
I shall follow with interest.

Posted by martinbishop over 2 years ago (Flag)
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Overall, I believe this would be a great idea. The Plant List can be quite frustrating sometimes, e.g. when two synonyms both have "unresolved" status. As a marine biologist, I am not very familiar with Fauna Europaea, but I guess it would be useful for terrestrial groups not covered by WoRMS.

Posted by duarte over 2 years ago (Flag)
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@kueda A little off topic, but there are also databases for Hawaiian, Micronesian and Marquesas islands plants. The IUCN has been using it as a source and it's managed by the Smithsonian. http://botany.si.edu/pacificislandbiodiversity/hawaiianflora/query2.cfm

Posted by duarte over 2 years ago (Flag)
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Another one of the problem with TPL is that there are no authors mentioned. As already suggested, I would consider TPL as a valid alternative for European plant taxa in the case of a lacking treatment in Euro+Med.

Conflicts between different taxonomy databases are unavoidable. In those cases it will be important to discuss among curators in order to try to make the decision that should be at the same time the most scientifically rigorous and the most user friendly.
In this sense, I think that not all taxonomic changes could be perceived as bothersome but, actually, in the case they are well documented as far as the literature is concerned, they could be a way to increase the knowledge of a given taxonomic case.

Posted by blue_celery over 2 years ago (Flag)
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This is a world checklist for Lepidoptera Geometridae:
http://lepbarcoding.org/geometridae/species_checklists.php

Posted by claudioflamigni over 2 years ago (Flag)
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For the taxon-specific global lists I would really like you to reconsider your source for birds. It would be so great if you would start following the IOC taxonomy. Since this list not only keeps its scientific names up-to-date but also it's vernacular names. This meand we talk in the entire world about the same species in all languages!
http://www.worldbirdnames.org/

Posted by wouterteunissen over 2 years ago (Flag)
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there are of course many lists, but many of them are outdated, especially for the more obscure groups, there afe probably many taxonomic changes but no up to date lists... So what to do then?

Posted by wouterteunissen over 2 years ago (Flag)
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It would be wonderful if AlgaeBase and Species Fungorum would be added too as acceptable databases. And the Geometridae list above would be great...

Posted by vilseskog over 2 years ago (Flag)
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@marcoschmidtffm - What do you mean that TPL is no longer updated? I hadn't heard that, and if so, that is really a problem. Feel free to fill me on off-line (lena.struwe@rutgers.edu). Thanks!

Posted by vilseskog over 2 years ago (Flag)
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@vilseskog The World Register of Marine Species (WoRMS) uses AlgaeBase as a source of records, so adding Algaebase would not necessarily be crucial. Species Fungorum is already mentioned in the curator guide:
http://www.inaturalist.org/pages/curator+guide

Posted by duarte over 2 years ago (Flag)
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@vilseskog Lately, when I wanted to give feedback on a small mistake in TPL, I was informed, that "tpl is unfortunately no longer maintained. All the updated data can soon be found on Plants of the World Online (POWO)" - but it may be worth contacting Kew for further details, especially concerning IDs in TPL and POWO - POWO seems to use the IPNI IDs.

Posted by marcoschmidtffm over 2 years ago (Flag)
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Aha - I understand - hopefully POWO will include better referencing! I will check with my friends in London. I am also going to the International Botanical Congress and the Nomenclature session there in July, so I am sure I will find out more. Hopefully TPL is being replaced with something better. It drove me crazy that they copyrighted the whole thing (TPL I mean), when it is based on work we taxonomists have done and slapping copyright on it hindered, not helped, research and use of the data.

That is great about AlgaeBase and WoRMS - I didn't know that. Species Fungorum might be mentioned, but I would love it iNaturalist would find the names so I don't have to add them manually. :)

Posted by vilseskog over 2 years ago (Flag)
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So I just looked at the Euro+Med database for the plant group I am most familiar with (having provided the latest worldwide classification and phylogeny), and there are several mistakes that make me wonder about the quality overall. I e-mailed the author and pointed out the mistakes and offered my help, but the gentians are easy compared to some of the larger families. Still, it is better to use this than nothing else, but there might be times when Euro+Med has to be overruled and there will be conflict with other databases.

Posted by vilseskog over 2 years ago (Flag)
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I think @johnnybirder has been also favouring a bird taxonomy other than Clements

Posted by jakob about 2 years ago (Flag)
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Thanks for tagging me @jakob. Absolutely yes on birds. It causes confusion and frustration among older users, and more importantly new users, to follow a taxonomy that is very region-specific, such as Clements. While North and South America generally follows Clements, the rest of the world generally relies on BirdLife International as their taxonomic authority. One of the issues is that someone first has to propose a chance to Clements to get the process started; its new world focus causes Clements to lag severely for non-American birds. In contrast, HBW/BirdLife International provides an up to date checklist for the entire world, including the new world. The stable URLs for BirdLife's taxonomy (which I dont think Clements provide) can be found through Handbook of Birds of the World http://www.hbw.com. As laid out at http://www.lynxeds.com/product/hbw-and-birdlife-international-illustrated-checklist-birds-world, HBW has been adopted by the European Union, United Nations, and IUCN (the latter obviously quite delayed). I thus believe a switch to HBW/BirdLife International's taxonomy will better facilitate interaction with birding authorities in Africa and beyond.

Posted by johnnybirder about 2 years ago (Flag)
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Apologies for coming late to this thread

My preference would be to use globally complete references anchored to a clade on the taxonomic tree whenever possible rather than stitching together regional references

Glancing at the curator guide, looks like we have that in effect for the following clades:
Mammals - The IUCN Red List of Threatened Species
Birds - The Clements Checklist
Amphibians - Amphibian Species of the world (+ internally managed deviations)
Reptiles - The Reptile Database
Fish - FishBase
Spiders - The World Spider Catalog
Insects
Ants - AntWeb
Dragonflies and Damselflies - World Odonata List
Bees - ITIS World Bee Checklist
Ground Beetles - Carabidae of the World

An example of references iNat is using that are not global include:
Butterflies - Pelham et al. (United States and Canada)
Vascular plants - Calflora (California)

While these global references may come with the cost of some local controversy, as iNat becomes more international, I think the benefits they bring for skirting regional discrepancies/confusion outweigh these costs. This thread gives a good example of what happens when a regional authority is used outside the region: https://www.inaturalist.org/observations/6429457

Also I've experimented with formally, sparingly, and explicitly deviating from global references with amphibians to accommodate regional preferences with amphibians (read more here: https://www.inaturalist.org/journal/loarie/11101-internal-reference-taxonomies-amphibian-pilot) and its working well.

With that in mind, ehat do folks think about trying to move to global references where such references are already available and of sufficient quality to adopt?
A good example of where we could do this might be Gymnosperms and Monocots by adopting Kew's http://wcsp.science.kew.org/ which are globally complete for these. (looping in @stevenkew)?

Are there any other good global authorities out there we should consider?

WoRMs is a great global reference, but its problematic with the above because its not explicitly linked to any clade (rather "Marine Invertebrates") - would we be able to rather be more explicit and say for example:
Echinodermata - WoRMs
Tunicata - WoRMs
etc.?

This leaves clades where there are no good global references available - of which there are many (e.g. lots of plant families and insect families). Here, it seems we have 3 options:
1) the regional-stitching approach (e.g. a 'butterflies of the new world' and 'butterflies of the old world' with some set of rules for tie breaking
2) the literature tracking free-for-all approach (which is what we're currently doing for fungi no?)
3) a global backbone (like GBIF)

My preference here would be to migrate towards relying on (3) rather than (1) + (2) for these poorly known clades. I suspect people would be loathe to relinquish regional sources, but I'm perhaps naively hopeful that we could channel that energy into getting more global references in use even if the clades are more restricted. For example, rather than 'butterflies of the new world' and 'butterflies of the old world' maybe we could adopt global references for some families and rely on GBIF for the gaps

Thoughts?

Posted by loarie about 2 years ago (Flag)
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nutcracker, Gymnosperms on Kew WCSP is complete and being actively maintained. Plant List is not actively maintained. My understanding is that Kew is merging WCSP and PlantList into http://www.plantsoftheworldonline.org/ which will be 'ready for showtime' ie globally complete and actively maintainted by 2020.

iNat is using Clements as the global reference for Birds. My preference is to focus on a plan clades where we have no global references rather than switching existing global references.

But if folks want to discuss switching from Clements to IOC, my personal feeling is that would be a very hard sell to the North American community using iNat (which currently dominates in terms of # users) but thats just my prediction. In any case looping in @cullen who works at Cornell Lab of O

Posted by loarie about 2 years ago (Flag)
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nutcracker - here's a link to the species level spreadsheets for each of the 12 families of Gymnosperms exported from WCSP https://www.dropbox.com/s/wyjlju000lgogp1/WCSP_gymnosperms.zip?dl=0
We're probably talking semantics here, but by globally complete I mean does the scope of the reference consider all extant species globally (ie they didn't leave out a genus or species from a certain location etc.). By that metric WCSP is complete for Gymnosperms. (by the same metric I acknowledge that WCSP is not complete for Vascular plants, hence 'World checklist of selected plant families'

If you mean how often do they update WCSP - my understanding is that it is actively maintained. But I'm not sure how actively. Also, Kew, like all taxonomic references, comes with the Kew-perspective on taxonomy. That means they might ignore certain papers and pick and choose from ones that offer conflicting taxonomic opinions. But both of these variables: (1) how actively is a reference maintained and (2) which taxonomic opinions a reference chooses to incorporate are different from completeness.

Having clarified by what I meant by complete, are we on the same page in agreeing that WCSP is complete for Gymnosperms?

Posted by loarie about 2 years ago (Flag)
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With WFO there should soon be a good backbone for all plants available: http://about.worldfloraonline.org/index.shtml

Posted by marcoschmidtffm about 2 years ago (Flag)
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@loarie WoRMS does have specific nested databases for several taxa, although they don't always have a separateinterface, so we can actually be more specific if you want. See: http://www.marinespecies.org/about.php

Posted by duarte about 2 years ago (Flag)
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duarte - thats perfect. Thanks!

nutcracker - I put iNat's gymnosperms and Kew gymnosperms in this spreadsheet https://docs.google.com/spreadsheets/d/10e3QgCam8rikt_y17Wh3XvY2-auTFIyqwq_2tbME1oo/edit?usp=sharing
I added a blank column for conifersdotorg (conifersdotorg_name) can you fill that in? This will allows us to fill in the surface specific discrepancies in the sources so we can contrast the sources with specific examples (extant species only please - e.g. no hybrids, extinct taxa, or ssp/var)
Thanks!

Posted by loarie about 2 years ago (Flag)
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Great thanks - For the time being - lets just code the spreadsheet as I've started doing (also if anyone else wants to help!). Specifically, I mean matching up iNat to the WCSP names via swaps/splits/merges + any notes. And also filling in the columns and doing similarly for http://www.conifers.org/zz/gymnosperms.php) Then once its completely coded (ie all taxa are matched up between iNat, WCSP, and GD) we can discuss particular discrepancies and a the costs/benefits of adding global references for Gymnosperms and if so which one (WCSP, GD, or some cherrypicked hybrid of multiple references). Jakob if you'd like me to make a new Gymnosperms thread to not sidetrack your Europe taxonomy thread - happy to do so.

Posted by loarie about 2 years ago (Flag)
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Just to give a sense for where we'd be going with this Gymnosperm exercise, I fully coded the family Araucariaceae for both WCSP and GD. So were we to adopt a global reference for that genus (rather than the regional stitching approach), whether we went with WCSP or GD we'd probably want to:
1. merge Agathis robusta (sensu stricto) & Agathis spathulata into Agathis robusta (sensu lato)
2. merge Agathis dammara (sensu stricto) & Agathis philippinensis into Agathis dammara (sensu lato)

However, the following 3 changes would bring iNat in line with WCSP but out of line with GD. So whether we were to make them or not would depend on which reference we would be using.
3. swapping Agathis labillardieri into Agathis labillardierei
4. merging Agathis borneensis (sensu stricto) & Agathis endertii into Agathis borneensis (sensu lato)
5. merging Agathis moorei (sensu stricto) & Agathis corbassonii into Agathis moorei (sensu lato)

Similarly, the following 1 change would bring iNat in line with GD but out of line with WCSP.
6. splitting Araucaria muelleri (sensu lato) into Araucaria goroensis & Araucaria muelleri (sensu stricto)

Also, another advantage of WCSP is that they include machine readable distribution information which is also very useful in terms of making sense of taxonomic messes like these.

Posted by loarie about 2 years ago (Flag)
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Hi all, this is a very interesting thread I will have to read more carefully.
I quickly wanted to give some information from the GBIF perspective on this.

1) GBIF has engaged with the Catalogue of Life on a new CoL+ project to join forces and establish a clearinghouse for nomenclature and taxonomy. As an outcome we hope to build the classic CoL and the GBIF Backbone through the same infrastructure and underlying data, integrating nomenclatural resources like IPNI

2) The GBIF Backbone is algorithmically created based on these resources, listed in descending priority, which are all available on their own via GBIF: https://github.com/gbif/checklistbank/blob/master/checklistbank-nub/nub-sources.tsv

3) Within CoL+ we want to join forces with World Flora Online, Kew and others to all work on a shared global plants taxonomy. Maybe that would be sth of interest for iNat too and even room for active contribution?

Posted by markus about 2 years ago (Flag)
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Thanks for joining this discussion, @markus, would be good to get more input from you / GBIF. Maybe @dhobern wants to chime in as well?

@loarie I'd prefer if we could use this thread to discuss the general way forward with respect to iNat's taxonomic backbones, so if the gymnosperm discussion is likely to continue for some while, I suggest to open a new thread.

A few thoughts and suggestions:

- Overall, I'd much prefer global over regional lists, and would suggest to define that as an overarching principle how to select taxonomic backbones. In that case, we'll probably end up with a pretty long list of external resources, and that calls for a dedicated space on iNat (see suggestion below).

- In that context, it might be useful to be clear about what the purpose of taxonomic backbones is, and which aspects are considered of prime importance. For instance, if unambiguous data exchange with GBIF is a top priority, then using GBIF's taxonomic backbone would seem to be a good solution (or future target).

- My bird expertise is pretty limited, so I can't make a solid judgement of Clements vs IOC, but I'm hearing the same comment over and over again - that Clements is heavily biased by a North American perspective, and IOC the accepted global list. If that's indeed the case, why not move to IOC to strengthen iNat's global approach?

- I think it would be tremendously helpful to have a section of the Help Pages dedicated to just the taxonomic backbones used by iNat. These "Taxonomic Pages" would link out to the various global (and regional) resources, which are often very useful when identifying stuff on iNat (eg "Which Nephila species are listed by the World Spider Catalogue for Africa?"). Taxonomic Pages could be continuously updated and expanded by the curator community (maybe with a formal mechanism that approves taxonomic backbones for iNat), and also host linked discussion pages where curators have a forum to propose changes, deviations etc before these are implemented in iNat's taxonomy (in continuation of some of the comments here, and posts dedicated to amphibians, mammals and odonates ).

- Stitching regional lists together is likely to cause conflict - think of regional lists adopted in Europe vs North America, with quite a few species in common. I'd be favouring global lists but wonder if GBIF's backbone taxonomy would already have the "cleanliness" of well-curated regional lists to fill taxonomic gaps. I'm sure these issues have been popping up time and again, and that folks at GBIF and other global taxonomy projects have come up with solutions for that.

Posted by jakob about 2 years ago (Flag)
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Hi @jakob - great ideas and I agree with everything you say here.

I separated out the Gymnosperm conversation here: https://www.inaturalist.org/journal/loarie/11992-gymnosperms-ready-for-global-taxonomic-consensus

I'm personally very interested in the idea of using GBIF as the global backdrop with more rigorous community managed gloabal taxonomies for certain nodes (e.g. Gymnosperms). But the ruffling feathers issue you raise from regional differences is a big one. I think your ideas about taxonomic and help pages could really help foster communication and buy-in for more global taxonomies.

Posted by loarie about 2 years ago (Flag)
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Online databases often are not updated so frequently, sometimes not at all once published. So no matter if we will be in line with something and out of line with something else.
IMHO we should aim at being as much as possibe up-to-date with nomenclature and as much as rigorous from a scientific point of view.

Posted by blue_celery about 2 years ago (Flag)
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We in the Biodiversity Informatics & Spatial Analysis team at Kew have read the correspondence with great interest. We thought it might be useful to give an update on the nomenclatural and taxonomic resources at Kew; our response does not cover every point raised but we hope it will aid the discussion and clarify some of the issues raised.

Kew curates three major resources:
The International Plant Names Index (IPNI) with Harvard – a full-time curatorial team scan the literature to find newly published names. We have just released a beta version of IPNI and would be very pleased to have your feedback http://beta.ipni.org/
The World Checklist of Selected Plant Families (WCSP) – builds on the IPNI and is managed and maintained by Rafaël Govaerts http://wcsp.science.kew.org/about.do#history
Index Fungorum – curated by Paul Kirk with the longer-term plan of it being managed and maintained like IPNI at Kew.

The Plant List is different It is supported by Kew but has not been updated since 2013 (although the data is from 2012) however, we plan to change this. We are in the process of building a sustainable and updated TPL product based on the Plants of the World Online (POWO) Names backbone. The POWO names backbone is made up of managed names from IPNI and taxonomy from the World Checklist of Selected Plant Families (WCSP). There is an ongoing matching process between these 2 data sources. When a names is matched, it becomes available for the POWO backbone. The POWO backbone is currently an internal resource but our aim is to develop a new version of TPL based on this with an API to make it available to users outside Kew. The backbone is complete to family and genus level (some of the generic taxonomy comes from Kew’s Vascular Plant Families and Genera database where there are known gaps). The next data refresh in late November will reflect the matching work that has been going on over the summer, and POWO will include 99% of accepted species names over 95% of synonym species names from WCSP. We will also be providing a reconciliation service for PoWO names to compliment the current IPNI names service http://rbgkew.github.io/doc/reconciliation_index.html

In relation to the World Checklist of Selected Plant Families specifically:
WCSP is complete for all names entered in IPNI until 31 December 2016.
WCSP is 99.99% complete for species names and accepted (validly published) names.
WCSP is >90% complete for all names it covers.

WCSP contains about 40% of all Vascular plants.
WCSP+A-Z are about 96% complete for the taxa they cover.
WCSP+A-Z are about 85% complete for all Vascular plants.

As a general comment on the differences between WCSP, POWO, CoL, EURO+MED, GBIF, EOL, TPL...
We think it is important to flag that many of the names in those databases come from WCSP and the only reason there are discrepancies is because of the time it takes for a name change in WCSP to filter through to other databases. Take for example:

Psidium sartorianum was yesterday sunk into Psidium oligospermum:
http://wcsp.science.kew.org/nonacceptedRef.do?name_id=166919
this will take 2-3 months to go into POWO although the process will speed up as we continue to work on developing the POWO names backbone:
http://plantsoftheworldonline.org/taxon/urn:lsid:ipni.org:names:601026-1
about 2-3 years before it is in CoL:
http://www.catalogueoflife.org/col/details/species/id/3923be5d7a8a2d5fca1bb1990297591e
4-5 years before it gets into GBIF and EOL:
https://www.gbif.org/species/5420336
http://eol.org/pages/5455331/literature
will remain unchanged in TPL until TPL1.1 is replaced by a dynamic checklist:
http://www.theplantlist.org/tpl1.1/record/kew-166919

In all, we appreciate our nomenclatural and taxonomic resources are not perfect but Kew is putting substantial resource into them both in terms of development and curation. Finally, I would like to say that after lengthy discussion over many years, Kew now releases its data under CC-BY which is a huge step forward.

Posted by ambarker almost 2 years ago (Flag)
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Just discovered this GloBIS website www.globis.insects-online.de

Would be great if butterfly folks could check if that could be a global taxonomic backbone for butterflies. @hkmoths @chrisvanswaay. Also triggered by the issue of conflicting higher taxonomies here www.inaturalist.org/observations/6429457

Posted by jakob almost 2 years ago (Flag)
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@jakob - I'm not really in touch with the butterfly scene. However, the Maniola case shows there remains a lot of uncertainty in the classification situation regarding butterflies (don't even get me started on the rest of the Lepidoptera).

I absolutely agree that wherever one exists, a global primary reference source should be the basis of the iNat database. My understanding is that in the Nymphalidae, the Nymphalid Systematics Group is at the"cutting edge" and is producing literature pertaining to components of the Nymphalid classification, aiming to obtain a global understanding. The question therefore, in my mind, is what should iNat do about the situation whilst awaiting the global classification? Of the 5 options posted at www.inaturalist.org/observations/6429457 by @loarie I would consider options 2 or 4 as most viable, and welcome a dedicated forum approach , wherein relevant curators should be voicing their concerns.

For moths, there are a number of global online sources, all based on primary literature. Some are constantly updated, some are now static (the tineid database was based upon the work of the late Gaden Robinson, and I suspect no one will take up the reins anytime soon), though I would recommend these sources of info as they are as good as we have for now.
So here is the global list of online sources I have been using for iNat:
LepIndex - not good for higher classification, but good for checking validity of species names and synonyms. reputedly being updated at the moment,, which is needed as it's over a decade out of date. - http://www.nhm.ac.uk/research-curation/research/projects/lepindex/
Lepidoptera Genera - updated in 2016; lists all Lepidoptera genera and their statuses. - http://www.nhm.ac.uk/research-curation/research/projects/butmoth/
Families
Hepialidae - http://johngrehan.net/index.php/hepialidae/ (to 2017 - a personal website by the leading global authority on the family; don't know how long this site will be operational. Based on published primary literature)
Nepticulidae & Opostegidae - http://nepticuloidea.info/ (to October 31st, 2016)
Tineidae - no longer operational.
Gracillariidae - http://www.gracillariidae.net/ (last updated: 08 August 2017)
Sesiidae - http://www.sesiidae.net/sesiidae.htm (last updated: 12 March 2017)
Choreutidae - http://choreutidae.myspecies.info/ (active to late 2014)
Tortricidae - http://www.tortricidae.com/catalogue.asp (to early 2014)
Pyraloidea - http://www.pyraloidea.org/ (website) & http://globiz.pyraloidea.org/ (database); (latest update, 12 Nov 2017)
Sphingidae - http://sphingidae.myspecies.info/ (latest update, 10 Nov 2017)
Erebidae: subfamily Aganainae - http://www.aganainae.nl/ (latest update, 27 July 2016)

hope this helps. Lepidoptera have a very long way to go before getting the basic global inventory even close to being sorted.

Posted by hkmoths almost 2 years ago (Flag)
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Super useful, @hkmoths!

I think it's time for iNat to have a Help Page for users and curators alike that is dedicated to, and explains, the external taxonomies used by iNat (thus expanding the bits found at https://www.inaturalist.org/pages/curator+guide#policies).

Posted by jakob almost 2 years ago (Flag)
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@jakob Good this discussion is going. I leave it up to the taxonomy experts to find a way out of this. Good luck!

Posted by chrisvanswaay almost 2 years ago (Flag)
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I just wanted to thank @ambarker for all the detailed explanations above. In my experience, there are a lot of neotropical plants missing from iNat, and I hope they will be available sooner than later.

Posted by vilseskog almost 2 years ago (Flag)
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@bbinsecte recently spotted me that FE was actually pretty obsolete concerning Opiliones - and maybe other Arachnids - for which GBIF would fit better.
Non-Spiders Arachnids are currently no covered by any specific Authority, and here follow FE, that appears unsatisfying for some points : e.g. Leiobunum appenninicum / Neolima appenninica...

Asking then to Arachnids specialists, from Europe & outside, @pdubois @sclerobunus @tigerbb : what would you think about using GBIF, rather than FE, as a Taxonomical Authority for European Opiliones ? or event oustide Europe ? or even for other/wider groups (other Arachnids, all non-Spider Arachnids ?)

Or maybe would you have a better reference to propose ?

Posted by fabienpiednoir 11 months ago (Flag)
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For spiders, the most up to date resource is the World Spider Catalog
https://wsc.nmbe.ch/
For opiliones, this is more difficult as the taxonomy of this group is still quite instable.
In France, we've got the INPN Taxref that covers all groups, but only for french species.
https://inpn.mnhn.fr/programme/referentiel-taxonomique-taxref?lg=en

It seems that GBIF uses those references, so it may be a good solution for a world wide scope.

Posted by pdubois 11 months ago (Flag)
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For arachnids... I come from a country that uses the imperial system instead of metric, so I crave standardization. That said, there may be some good global taxonomic resources for individual non-spider arachnid orders, but I am not aware of them. @danni_sherwood may know if one exists for Theraphosidae. But my guess is that GBIF would be our best bet, at least for the smaller orders, because there are several, and they are unlikely to have another authority.

Posted by tigerbb 11 months ago (Flag)
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For Spiders, WSC is already used as an authority. For the others, for now, GBIF seems to satisfy everybody...

Posted by fabienpiednoir 11 months ago (Flag)
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For European spiders I strongly suggest that the Natural History Museum of Bern's "Spiders of Europe" be utilised: https://araneae.nmbe.ch/

It is a "sister site" of the World Spider Catalog which is the backbone for listing taxonomic changes and positions in Araneae worldwide. The WSC is already used here as the standard for spider taxonomy on the world wide stage. Spiders of Europe would be a good resource for continent level organisation.

Just some notes on other arachnid groups:

For Opiliones I would recommend GBIF as it follows the world catalogues produced by Adriano Kury of the MNRJ (who does very thorough work). You will find disparity in the higher level classification of Scorpiones because there are two current classification systems accepted by different groups of workers but again you may want to consider GBIF as a "backbone". Since my expertise is in spiders I would recommend consulting other taxonomists for those two groups, namely @sjl197 (Opiliones) and @lorenzo_prendini (Scorpiones)

Posted by danni_sherwood 11 months ago (Flag)

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