TG2-AMENDMENT_SCIENTIFICNAMEID_FROM_TAXON

[iDigBioBot]

TestField	Value
GUID	431467d6-9b4b-48fa-a197-cd5379f5e889
Label	AMENDMENT_SCIENTIFICNAMEID_FROM_TAXON
Description	Proposes an amendment to the value of dwc:scientificNameID if it can be unambiguously resolved from bdq:sourceAuthority using the available taxon terms.
TestType	Amendment
Darwin Core Class	dwc:Taxon
Information Elements ActedUpon	dwc:scientificNameID
Information Elements Consulted	dwc:taxonID
	dwc:acceptedNameUsageID
	dwc:originalNameUsageID
	dwc:taxonConceptID
	dwc:scientificName
	dwc:higherClassification
	dwc:kingdom
	dwc:phylum
	dwc:class
	dwc:order
	dwc:superfamily
	dwc:family
	dwc:subfamily
	dwc:tribe
	dwc:subtribe
	dwc:genus
	dwc:genericName
	dwc:subgenus
	dwc:specificEpithet
	dwc:infraspecificEpithet
	dwc:cultivarEpithet
	dwc:vernacularName
	dwc:scientificNameAuthorship
	dwc:taxonRank
Expected Response	EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; INTERNAL_PREREQUISITES_NOT_MET if dwc:scientificNameID is bdq:NotEmpty, or if all of dwc:scientificName, dwc:genericName, dwc:specificEpithet, dwc:infraspecificEpithet, dwc:scientificNameAuthorship, and dwc:cultivarEpithet are bdq:Empty, FILLED_IN the value of dwc:scientificNameID for an unambiguously resolved single taxon record in the bdq:sourceAuthority through (1) the value of dwc:scientificName or (2) if dwc:scientificName is bdq:Empty through values of the terms dwc:genericName, dwc:specificEpithet, dwc:infraspecificEpithet, dwc:scientificNameAuthorship and dwc:cultivarEpithet, or (3) if ambiguity produced by multiple matches in (1) or (2) can be disambiguated to a single Taxon using the values of dwc:subtribe, dwc:tribe, dwc:subgenus, dwc:genus, dwc:subfamily, dwc:family, dwc:superfamily, dwc:order, dwc:class, dwc:phylum, dwc:kingdom, dwc:higherClassification, dwc:taxonID, dwc:acceptedNameUsageID, dwc:originalNameUsageID, dwc:taxonConceptID, dwc:taxonomicRank, and dwc:vernacularName; otherwise NOT_AMENDED
Data Quality Dimension	Conformance
Term-Actions	TAXONID_FROM_TAXON
Parameter(s)	bdq:sourceAuthority
Source Authority	bdq:sourceAuthority default = "GBIF Backbone Taxonomy" {[https://doi.org/10.15468/39omei]} {API endpoint [https://api.gbif.org/v1/species?datasetKey=d7dddbf4-2cf0-4f39-9b2a-bb099caae36c&name=]}
Specification Last Updated	2023-09-17
Examples	[dwc:taxonID="", dwc:scientificNameID="", dwc:acceptedNameUsageID="", dwc:originalNameUsageID="", dwc:taxonConceptID="", dwc:scientificName="Chicoreus palmarosae (Lamarck, 1822)", dwc:higherClassification="", dwc:kingdom="Animalia", dwc:phylum="Mollusca", dwc:class="Gastropoda", dwc:order="", dwc:family="Muricidae", dwc:subfamily="", dwc:genus="Chicoreus", dwc:genericName="Chicoreus", dwc:subgenus="", dwc:infragenericEpithet="", dwc:specificEpithet="palmarosae", dwc:infraspecificEpithet="", dwc:cultivarEpithet="", dwc:vernacularName="", dwc:scientificNameAuthorship="(Lamarck, 1822)", dwc:taxonRank="", bdq:sourceAuthority=”marinespecies.org”: Response.status=FILLED_IN, Response.result=dwc:scientificNameID="urn:lsid:marinespecies.org:taxname:208134", Response.comment="dwc:scientificName matched to unique taxon record in WoRMS, exact match on name and authorship. Resolvable at https://marinespecies.org/aphia.php?p=taxdetails&id=208134"]
	[dwc:scientificNameID="", dwc:taxonID="", dwc:acceptedNameUsageID="", dwc:originalNameUsageID="", dwc:taxonConceptID="", dwc:scientificName="Graphis", dwc:higherClassification="", dwc:kingdom="", dwc:phylum="", dwc:class="", dwc:order="", dwc:family="", dwc:subfamily="", dwc:genus="", dwc:genericName="", dwc:subgenus="", dwc:infragenericEpithet="", dwc:specificEpithet="", dwc:infraspecificEpithet="", dwc:cultivarEpithet="", dwc:vernacularName="", dwc:scientificNameAuthorship="", dwc:taxonRank="": Response.status=NOT_AMENDED, Response.result=, Response.comment="dwc:scientificName="Graphis" is ambiguous as could be either a lichen or a gastropod."]
Source	FP-Akka
References	GBIF Secretariat (2023) GBIF Backbone Taxonomy. Checklist dataset. https://doi.org/10.15468/39omei
Example Implementations (Mechanisms)	Kurator/FilteredPush sci_name_qc Library, FP-KurationServices, Arctos, MCZbase, Symbiota
Link to Specification Source Code	https://github.com/FilteredPush/sci_name_qc/blob/v1.1.2/src/main/java/org/filteredpush/qc/sciname/DwCSciNameDQ.java#L397 https://github.com/FilteredPush/sci_name_qc/blob/v1.1.2/src/main/java/org/filteredpush/qc/sciname/DwCSciNameDQ.java#L476
Notes	Return a result with no value and a Result.status of NOT_AMENDED with a Response.comment of ambiguous if the information provided does not resolve to a unique result (e.g. if homonyms exist and there is insufficient information in the provided data, for example using the lowest ranking taxa in conjunction with dwc:dwc:scientificNameAuthorship, to resolve them). When referencing a GBIF taxon by GBIF's identifier for that taxon, use the the pseudo-namespace "gbif:" and the form "gbif:{integer}" as the value for dwc:scientificNameID.

[iDigBioBot]

Comment by Paul Morris (@chicoreus) migrated from spreadsheet:
Moving from scientificName as a string to a link to a guid in a taxonomic or nomenclatural authority is key for moving towards linked open data and other semantic delivery of biodiversity data. There is almost never enough data in flat Darwin Core to fill in any of the other ID terms in the Taxon class, but it is often possible to link scientific name strings to nomenclatural or taxonomic records.

[godfoder]

We should add taxonRank to the list of fields for this and #70 . It is especially important for the interpretation of monomials in scientific name absent other supporting data.

[chicoreus]

@godfoder I concur. Do we need to specify a more complex set of prerequisites?

[chicoreus]

A couple of issues for implementation:

Acton to take when taxonID is NOT_EMPTY: The specification is mute on what action to take when dwc:taxonID has a value. Since other tests specify CHANGED only if term that is proposed to be amended is NOT_EMPTY, the implication is that an amendment is to be proposed, for purposes such as conforming taxonID values to a national authority. This should probably be spelled out in the notes section.

Extraneous terms in the list of Information Elements: The specification states that a proposed amendment should be based on "on the basis of the value of the lowest ranking not EMPTY taxon classification terms dwc:scientificName, dwc:scientificNameAuthorship, dwc:kingdom, dwc:phylum, dwc:class, etc.", with @godfoder's comment clearly indicating that taxonRank should be included in this list. The notes imply that none of the other ID terms (dwc:scientificNameID, dwc:acceptedNameUsageID, dwc:originalNameUsageID, dwc:taxonConceptID) should be included in this analysis, so it seems that they shouldn't be included in the informationElements, unless there is a clear specification of how to include them to infer a value of taxonID. Also, neither dwc:higherClassification nor dwc:vernacularName are included in the specification, and thus don't seem to fit in the list of information elements.

[ArthurChapman]

Further to the logic of @chicoreus - I don't understand the inclusion of dwc:scientificNameAuthorship as it isn't a taxon classification term in the hierarchy, and that and that field alone could not supply a taxonID.

[chicoreus]

@ArthurChapman I see scientificNameAuthorship as an essential term for identifying which taxonID to use, it can often disambuguate homonyms and if the authorship string associated with the source record for taxonID isn't the same as the authorship string in a record under consideration, then something likely isn't correct and an assertion of of a taxonID match is not a good one to make.

[tucotuco]

Not yet! There are some questions still to be answered (the email I sent around on #57 and #70) - for example

1. on treatment of dwc:cultivarEpithet different to dwc:infraspecificEpithet (I believe they shouldn't be differently treated - @tucotuco to clarify use of dwc:cultivarEpithet) - see my comment of two days ago

My understanding is that a cultivarEpithet should be as determinant of a Taxon as an infraspecificEpithet is and treated in the same way.

2. and whether or not the higher categories have TAXONIDs. From my email
   "I am still not fully convinced re TAXONID and higher level taxa. Does the sourceAuthority (GBIF?) give a TAXONID for a family name?I am not familiar enough with TAXON ID to know. If they don't then I accept @chicoreus arguments. But if they do, and a record has only a name at the Family level with no information at a lower level (i.e. I have only been able to identify this record to Family). If the sourceAuthority gives a Taxon ID for the Family - then why would be not use that TAXONID for the record.
   This is particularly relevant as the Botanical Code defines a taxa as
   "Taxonomic groups at any rank will, in this Code, be referred to as taxa (singular: taxon)."
   In the Zoological Code:
   "A taxonomic unit, whether named or not: i.e. a population, or group of populations of organisms which are usually inferred to be phylogenetically related and which have characters in common which differentiate (q.v.) the unit (e.g. a geographic population, a genus, a family, an order) from other such units. A taxon encompasses all included taxa of lower rank (q.v.) and individual organisms. The Code fully regulates the names of taxa only between and including the ranks of superfamily and subspecies"
   The Zoological Code treats a family name as a taxon
   "family name or name of a family
   A scientific name of a taxon at the rank of family."
   Darwin Core definition
   "A group of organisms (sensu http://purl.obolibrary.org/obo/OBI_0100026) considered by taxonomists to form a homogeneous unit." It gives the example of "The genus Truncorotaloides as published by Brönnimann et al. in 1953 in the Journal of Paleontology Vol. 27(6) p. 817-820."

I agree with @chicoreus about the case where dwc:family (and no lower rank) is populated and dwc:scientificName is not, for the simple fact that the Taxon is ambiguous. Specifically, it MIGHT be the family, but it might be something in the family. Probably way too subtle for most people to worry about, but I think it's correct.

[ArthurChapman]

OK - if we accept the rasoning of @chicoreus and @tucotuco

INTERNAL_PREREQUISITES_NOT_MET if dwc:taxonID is not EMPTY or if all of, dwc:scientificName, dwc:genericName, dwc:specificEpithet, dwc:infraspecificEpithet, dwc:scientificNameAuthorship, and dwc:cultivarEpithet are EMPTY, AMENDED the value of taxonID for an unambiguously resolved single taxon record in the specified source authority service through (1) the value of dwc:scientificName or (2) if dwc:scientificName is EMPTY through values of the terms dwc:genericName, dwc:specificEpithet, dwc:infraspecificEpithet, dwc:scientificNameAuthorship and dwc:cultivarEpithet), or (3) if ambiguity produced by multiple matches in (1) or (2) can be disambiguated to a single Taxon using the values of dwc:subgenus, dwc:genus, dwc:subfamily, dwc:family, dwc:order, dwc:class, dwc:phylum, dwc:kingdom, dwc:higherClassification, dwc:scientificNameID, dwc:acceptedNameUsageID, dwc:originalNameUsageID, dwc:taxonConceptID, dwc:taxonomicRank, and dwc:vernacularName); otherwise NOT_AMENDED

If accepted it appears that we can take dwc:genericName and dwc:infragenericEpithet out of Information Elements

Note:

1. I have taken dwc:cultivatedEpithet and dwc:taxonRank out of the INTERNAL_PREREQUISTES_NOT_MET
2. I have changed the wording of (1) and (2) around dwc:cultivatedEpithet in the AMENDED area to treat it the same as dwc:infraspecificEpithet
3. I have taken dwc:taxonRank out of (2)
4. I have added dwc:subfamily to (3)
5. Some other minor wording and spelling corrections

[Tasilee]

I have to defer to @chicoreus, @ArthurChapman and @tucotuco on this. I will apply @ArthurChapman's latest Expected Response, with a few more tweaks.

[Tasilee]

• I have corrected a stray bracket in the ER.
• Quoting @ArthurChapman "If accepted it appears that we can take dwc:genericName and dwc:infragenericEpithet out of Information Elements". True for dwc:infragenericEpithet (done) but not so for dwc:genericName as it is in the current ER.

Are we all happy with the specifications on this one now?

[Tasilee]

Changed "AMENDED" to "FILLED_IN" in accordance with discussions April 16.

[Tasilee]

Amended Example to align with @chicoreus comments in email 17th June 2022.

[chicoreus]

So the text of cultivarEpithet should also be found in scientificName?

…

On Sun, 13 Mar 2022 22:37:49 -0700 John Wieczorek ***@***.***> wrote: > 1. on treatment of dwc:cultivarEpithet different to > dwc:infraspecificEpithet (I believe they shouldn't be differently > treated - @tucotuco to clarify use of dwc:cultivarEpithet) - see my > comment of two days ago My understanding is that a cultivarEpithet should be as determinant of a Taxon as an infraspecificEpithet is and treated in the same way.

[tucotuco]

So the text of cultivarEpithet should also be found in scientificName?

Yes, I think it should. But for a definitive answer it is best to ask someone such as @mdoering and @ nielsklazenga.

[ArthurChapman]

@nielsklazenga - any comments? [space inadvertently included in last post by @tucotuco

[nielsklazenga]

Regarding cultivarEpithet, yes, that is part of the scientificName string.

[Tasilee]

Why don't we have an "EXTERNAL_PREREQUISITES_NOT_MET" if we reference bdq:sourceAuthority?!

I've added it as otherwise it will stuff up the test data work.

[Tasilee]

Changed Parameter(s) to "bdq:sourceAuthority" as per discussions 12th June 2023

[ArthurChapman]

I have added to the Notes to be consistent with #71:

"When referencing a GBIF taxon by GBIF's identifier for that taxon, use the the pseudo-namespace "gbif:" and the form "gbif:{integer}" as the value for dwc:taxonID."

[chicoreus]

Will need to include the new terms dwc:superfamily, dwc:tribe, dwc:subtribe tdwg/dwc#65 tdwg/dwc#45 tdwg/dwc#46

[Tasilee]

Added the terms dwc:superfamily, dwc:tribe, dwc:subtribe to the Information elements and Expected response, and updated Specification Last Updated.

On this one, please check my Expected response.

[Tasilee]

Amended Source Authority values to align with @chicoreus syntax

From

bdq:sourceAuthority default = "GBIF Backbone Taxonomy" [https://doi.org/10.15468/39omei] |
| | API endpoint [https://api.gbif.org/v1/species?datasetKey=d7dddbf4-2cf0-4f39-9b2a-bb099caae36c&name=]

to

bdq:sourceAuthority default = "GBIF Backbone Taxonomy" {[https://doi.org/10.15468/39omei]} {API endpoint [https://api.gbif.org/v1/species?datasetKey=d7dddbf4-2cf0-4f39-9b2a-bb099caae36c&name=]}

[Tasilee]

Splitting bdqffdq:Information Elements into "Information Elements ActedUpon" and "Information Elements Consulted". Also changed "Field" to "TestField" and "Output Type" to "TestType".