Links to Global Register of Introduced and Invasive Species - United States of America (Contiguous) no longer show up

[gbif-portal]

Links to Global Register of Introduced and Invasive Species - United States of America (Contiguous) no longer show up

Links to Global Register of Introduced and Invasive Species - United States of America (Contiguous) no longer show up in GBIF backbone for species that had them until a week or so ago.

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User: See in registry System: Firefox 97.0.0 / Windows 10.0.0 Referer: https://www.gbif.org/species/160937834/verbatim Window size: width 1847 - height 1198 API log&_a=(columns:!(_source),filters:!(),index:'3390a910-fcda-11ea-a9ab-4375f2a9d11c',interval:auto,query:(language:kuery,query:''),sort:!())) Site log&_a=(columns:!(_source),filters:!(),index:'5c73f360-fce3-11ea-a9ab-4375f2a9d11c',interval:auto,query:(language:kuery,query:''),sort:!())) System health at time of feedback: OPERATIONAL

[ahahn-gbif]

(via email from helpdesk, 1.3.22):

Many thanks for contacting us about this (https://github.com/gbif/portal-feedback/issues/3955).

The reason for this is that dataset that this specific record came from (https://www.gbif.org/species/160937834/verbatim from https://www.gbif.org/dataset/6b64ef7e-82f7-47a3-8ddb-ec6794ea07d6) has been withdrawn by the initial publisher, as it is now published through a different dataset of the same scope and name: https://www.gbif.org/species/193827164 from https://www.gbif.org/dataset/32ad19ed-6b89-447a-9242-795c0897f345.

In the context of contributing datasets, taxon records are shown as published by the contributing data source. For the global overview, I would recommend to check the "GBIF backbone" version, in this case: https://www.gbif.org/species/5415039. You will find the references to the invasive status underneath the map.

[nonenmac]

Although “Global Register of Introduced and Invasive Species - United States (Contiguous)” is now showing up again in GBIF Backbone, all species that I have looked at so far show “Evidence of impact = No” when a week ago many of them showed “Evidence of impact = Yes” as would be expected for invasive species.

It looks like the names of the terms and their values have changed in the database, so they are no longer being interpreted correctly.

For example former term: “isInvasive = invasive” Is now: “degreeOfEstablishment = invasive (category D2)”

[ahahn-gbif]

reopening: some configuration issue(s) pending

[ahahn-gbif]

Pending internal verification: the term "isInvasive" comes from the Species Profile extension (https://rs.gbif.org/extension/gbif/1.0/speciesprofile_2019-01-29.xml). Will need to check whether adding the extension to the source file configuration and mapping the value "invasive" without further qualifiers is all that is needed to revert to the previous functionality.

This relates to the backbone species pages, like e.g. https://www.gbif.org/species/5960770, with the table on "Recorded as invasive in x countries or islands" underneath the map.

[nonenmac]

I've gone through several hundred non-native plant species that may be of concern in New York State and so far it appears that in all of them either:

degreeOfEstablishment = invasive (category D2) for most species for which "Evidence of impact" was formerly "Yes" degreeOfEstablishment = established (category C3) for most species for which "Evidence of impact" was formerly "No"

These don't strictly match the previous state of "Evidence of impact = Yes or No", but that's the general trend. From the documentation at http://rs.gbif.org/vocabulary/dwc/degree_of_establishment_2022-02-02.xml etc., it seems that D2 would map to "Evidence of impact = Yes" and C3 would be interpreted as "Evidence of impact = No" .

But ALL possible degrees of establishment should probably be mapped. For example "colonising (category D1)" and escpecially "widespread invasive (category E)" should also map to "Evidence of impact = Yes". Concepts in categories A, B, and C would probably all result in "Evidence of impact = No"

[nonenmac]

A related matter is that "Recorded as invasive in x countries or islands" (below the map) is often incorrect since it (x) includes all countries or islands that list the species as introduced, whether or not it is actually listed as invasive in those places. Maybe it should say "Recorded as introduced in x countries or islands" or something like that.

[ahahn-gbif]

ALL possible degrees of establishment should probably be mapped

@asimpson-usgs, would you like to comment on the mapping options for degreeOfEstablishment and isInvasive?

Concerning the header of that section in GBIF.org taxon pages ("Recorded as invasive in x countries or islands"), I remember a discussion around exactly that point. It was the reason for the "basis of evidence" flag being introduced, but I need to check whether there was a good reason not to label it "Recorded as introduced (...)" instead (@MortenHofft, @timhirsch, was there a rationale?). This label would be easy to change. The mapping will need to happen at the source side as sketched above, and then should show "Yes" under Basis of Evidence again.

[timhirsch]

Regarding the label on the taxon pages, this is something that has bugged me for a while and I am pretty sure there is no rationale for the use of 'invasive' here. Assuming that the number refers to countries/islands in which the species is included in the relevant GRIIS checklist, whether or not it is recorded as invasive, the label should certainly be 'Recorded as introduced ...' One thing just to clarify here is whether the number includes other checklists, e.g. for protected areas, in which case the label should reflect that appropriately. @dschigel may wish to confirm.

[asimpson-usgs]

In defense of the usage of ‘isInvasive’ term and its associated controlled vocabulary, @Tim @.***> and @dschigelhttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdschigel&data=04%7C01%7Casimpson%40usgs.gov%7C45b1ff3388d74ea25d8608da0037382d%7C0693b5ba4b184d7b9341f32f400a5494%7C0%7C0%7C637822534440003526%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=IKTijxowJiB0FTooDYDK6GT%2BkhF%2BNXsVhy0SULsHVzQ%3D&reserved=0, I’d like to draw your attention to the Groom et al. 2019 paper (https://doi.org/10.3897/biss.3.38084) and the resulting changes to Darwin Core terms described at https://dwc.tdwg.org/em/, https://dwc.tdwg.org/doe/, and https://dwc.tdwg.org/doe/ and adopted by TDWG in 2020. If GBIF prefers to insert “RecordedAs…” in order to fully map these terms, or if they need to be in a different Core or Extension implementation, please get on with it. (I don’t mean to be rude, but the GRIIShttps://griis.org/ community is anxious to get our terms fully mapped in the GBIF infrastructure as soon as is reasonably possible.)

Kind regards, Annie Simpson (she/her) biologist and information scientist Science Analytics and Synthesis Program U.S. Geological Survey Headquarters @.***, +1 703 648 4281 ORCID: 0000-0001-8338-5134https://orcid.org/0000-0001-8338-5134

From: timhirsch @.> Date: Monday, March 7, 2022 at 7:37 AM To: gbif/portal-feedback @.> Cc: Simpson, Annie @.>, Mention @.> Subject: [EXTERNAL] Re: [gbif/portal-feedback] Links to Global Register of Introduced and Invasive Species - United States of America (Contiguous) no longer show up (Issue #3955)

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Regarding the label on the taxon pages, this is something that has bugged me for a while and I am pretty sure there is no rationale for the use of 'invasive' here. Assuming that the number refers to countries/islands in which the species is included in the relevant GRIIS checklist, whether or not it is recorded as invasive, the label should certainly be 'Recorded as introduced ...' One thing just to clarify here is whether the number includes other checklists, e.g. for protected areas, in which case the label should reflect that appropriately. @dschigelhttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdschigel&data=04%7C01%7Casimpson%40usgs.gov%7C45b1ff3388d74ea25d8608da0037382d%7C0693b5ba4b184d7b9341f32f400a5494%7C0%7C0%7C637822534440003526%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=IKTijxowJiB0FTooDYDK6GT%2BkhF%2BNXsVhy0SULsHVzQ%3D&reserved=0 may wish to confirm.

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[ahahn-gbif]

Just to avoid confusion now: (a) @asimpson-usgs: the three USGS checklists published under the ISSG will need the SpeciesProfile extension mapped and the term "isInvasive" supplied in order for the "evidence of impact" for invasiveness to show in the GBIF species pages, as agreed before. Once this is done, the "Yes" values for the relevant species will show up again. No further changes here, and no introduction of any new terms implied. (b) the discussion on "Recorded as..." is around the table header, as in: a change in static text within GBIF's pages. It should not impact data publication in any way, and does have no influence on the mapping of terms or Darwin Core terminology

[dschigel]

Thanks @ahahn-gbif, hope (a) is clear and will get fixed for proper display of the data. as for choice of workds for the (b), I would actually consult with @qgroom.

[ahahn-gbif]

Just for illustration of points (a) and (b), from https://www.gbif.org/species/2465346:

[ahahn-gbif]

update: data and processing are now fixed for issue (a), with the Evidence of impact again interpreted and showing in the table on the species page. For issue (b), still waiting for confirmation on terminology to be used.

[melodie-mcgeoch]

Dmitry asked me to input here. I may be missing some of the nuances of the previous argument (and telling you what you no doubt already know), BUT: [b] in the screenshot above is cleary incorrect if [a] is correct. The two concepts are hierarchical in GRIIS - a species is invasive only if it is alien first. In the name GRIIS 'introduced' is synonymous with 'alien'. If a species has no "YES for isInvasive records" in GRIIS, then the species is alien and not invasive anywhere in the world. If a species is "YES for isInvasive" in only one country then it is invasive on a global checklist, but only alien (and not invasive) in other countries for which it is listed in the country checklists. SO - GRIIS 'operationalizes' the meaning of invasive in this way.

This is consistent with the non-operational, and for our purposes accepted, definition of "invasive alien species" according now to IPBES (consistent with the CBD definition) of IAS: _Species whose introduction and/or spread by human action outside their natural distribution threatens biological diversity, food security, and human health and well-being. “Alien” refers to the species’ having been introduced outside its natural distribution (“exotic”, “non-native” and “non-indigenous” are synonyms for “alien”). “Invasive” means “tending to expand into and modify ecosystems to which it has been introduced”. Thus, a species may be alien without being invasive, or, in the case of a species native to a region, it may increase and become invasive, without actually being an alien species._https://ipbes.net/glossary/invasive-alien-species

The concept of 'invasive' is scale dependent, which is part of what drives ongoing discussion of its definition. However, I think accepting that definitions of complex concepts naturally allow a range of interpretations is important. And that in order to achieve the level of comparability we are attempting to in the data world requires an operational definition.

[asimpson-usgs]

Thank you for chiming in, @melodie-mcgeoch. Clear usage of terms and their relationships is important here (and has not been universal in the invasive species science community).

While you are providing clear definitions, they are partly contradictory, and I had hoped you wouldn’t bring that last definition into the mix. Can’t we just leave it at this? “The two concepts are hierarchical in GRIIS - a species is invasive only if it is alien first.”

There is no need to bring into this discussion at this time the contradictory statement: “…in the case of a species native to a region, it may increase and become invasive, without actually being an alien species.” At least in the GRIIS-US (and all three sublists of the U.S. Register of Introduced and Invasive Species, for Alaska, Hawaii, and the Conterminous United States), native pest species (that are range-expanding and threatening) are not included.

[melodie-mcgeoch]

I absolutely agree @asimpson-usgs that for our purpose - “The two concepts are hierarchical in GRIIS - a species is invasive only if it is alien first.”

The general definition that we now have from IPBES will prevail for better or worse. The two are not contradictory though - it simply depends on how one defines the species pool you are working with/considering. In GRIIS we are working only with the set of species that are alien. In the IPBES definition both alien and non-alien species are encompassed in the consideration of species that have undesirable effects.