TG2-VALIDATION_TAXON_UNAMBIGUOUS

[iDigBioBot]

TestField	Value
GUID	4c09f127-737b-4686-82a0-7c8e30841590
Label	VALIDATION_TAXON_UNAMBIGUOUS
Description	Can the taxon be unambiguously resolved from bdq:sourceAuthority using the available taxon terms?
TestType	Validation
Darwin Core Class	dwc:Taxon
Information Elements ActedUpon	dwc:taxonID
	dwc:scientificName
	dwc:scientificNameID
	dwc:acceptedNameUsageID
	dwc:originalNameUsageID
	dwc:taxonConceptID
	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:infragenericEpithet
	dwc:specificEpithet
	dwc:infraspecificEpithet
	dwc:cultivarEpithet
	dwc:vernacularName
	dwc:scientificNameAuthorship
	dwc:taxonRank
Information Elements Consulted
Expected Response	EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; INTERNAL_PREREQUISITES_NOT_MET if all of dwc:scientificNameID, dwc:scientificName, dwc:genericName, dwc:specificEpithet, dwc:infraspecificEpithet, dwc:scientificNameAuthorship, dwc:cultivarEpithet are bdq:Empty; COMPLIANT if (1) dwc:scientificNameID references a single taxon record in the bdq:sourceAuthority, or (2) dwc:scientificNameID is bdq:Empty and dwc:scientificName references a single taxon record in the bdq:sourceAuthority, or (3) if dwc:scientificName and dwc:scientificNameID are bdq:Empty and if a combination of the values of the terms dwc:genericName, dwc:specificEpithet, dwc:infraspecificEpithet, dwc:cultivarEpithet, dwc:taxonRank, and dwc:scientificNameAuthorship can be unambiguously resolved to a unique taxon in the bdq:sourceAuthority, or (4) if ambiguity produced by multiple matches in (2) or (3) can be disambiguated to a unique Taxon using the values of dwc:tribe, dwc:subtribe, 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 and dwc:vernacularName; otherwise NOT_COMPLIANT
Data Quality Dimension	Conformance
Term-Actions	TAXON_UNAMBIGUOUS
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	2023-09-18
Examples	[dwc:taxonID="", dwc:scientificNameID="", dwc:acceptedNameUsageID="", dwc:originalNameUsageID="", dwc:taxonConceptID="", dwc:scientificName="Triplex rosaria Perry, 1811", dwc:higherClassification="", dwc:kingdom="Animalia", dwc:phylum="mollusca", dwc:class="Gastropoda", dwc:order="", dwc:family="Muricidae", dwc:subfamily="", dwc:genus="Chicoreus", dwc:genericName="Triplex", dwc:subgenus="", dwc:infragenericEpithet="", dwc:specificEpithet="rosarium", dwc:infraspecificEpithet="", dwc:cultivarEpithet="", dwc:vernacularName="", dwc:scientificNameAuthorship="Perry, 1811", dwc:taxonRank="",bdq:sourceAuthority=”marinespecies.org”: Response.status=RUN_HAS_RESULT, Response.result=COMPLIANT, Response.comment="dwc:scientificName matched to unique taxon record in WoRMS, unique fuzzy match on name and exact match on authorship. "]
	[dwc:taxonID="", dwc:scientificNameID="", 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=RUN_HAS_RESULT, Response.result=NOT_COMPLIANT, Response.comment="dwc:scientificName="Graphis" is ambiguous as could be either a lichen or a gastropod."]
Source	ALA, GBIF, CRIA
References	GBIF Secretariat (2023) GBIF Backbone Taxonomy. Checklist dataset. https://doi.org/10.15468/39omei
Example Implementations (Mechanisms)	Kurator/FilteredPush sci_name_qc Library
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#L796 https://github.com/FilteredPush/sci_name_qc/blob/v1.1.2/src/main/java/org/filteredpush/qc/sciname/DwCSciNameDQ.java#L843
Notes	There are any number of potential controlled vocabularies that might be used for this test, including local vocabularies and taxon specific vocabularies. If dwc:scientificNameID is empty, use dwc:scientificName and dwc:CultivarEpithet to search for a unique taxon. If dwc:scientificName is bdq:Empty, check with the terms that form atomic parts of it (dwc:genericName, dwc:specificEpithet, dwc:infraspecificEpithet, dwc:taxonRank, dwc:scientificNameAuthorship), and if more than one match is found, use the remaining terms to try to disambiguate to a single Taxon record. The terms dwc:subgenus, dwc:genus, dwc:family, dwc:order, dwc:class, dwc:phylum, dwc:kingdom, dwc:higherClassification, dwc:scientificNameID,, dwc:acceptedNameUsageID, dwc:originalNameUsageID, dwc:taxonConceptID should not be used to make a match if dwc:scientificNameID and dwc:scientificName or dwc:genericName, dwc:specificEpithet, dwc:infraspecificEpithet, dwc:taxonRank, dwc:scientificNameAuthorship are bdq:Empty. Note that test VALIDATION_SCIENTIFICNAME_FOUND (4c09f127-737b-4686-82a0-7c8e30841590) is a more specific test for a subset of Information Elements from this test.

[iDigBioBot]

Comment by Paul Morris (@chicoreus) migrated from spreadsheet:
There are homonyms created by the same author in the same year in the same higher taxon, indeed in a few cases in the same work, and in at least one case on the same page in the same work. Given Flat Darwin Core, there are cases where Darwin Core data could be filled out sufficently to disambiguate the homonyms, and other cases where Darwin Core terms for the text of a scientific name are unable to provide sufficient information for disambiguation. Including the taxon ids and referencing an id in a nomenclator or in a taxonomic authority can resolve these. The key to this test is whether or not the taxon terms can be uniquely related to the id of a nomenclatural act, however, outside vascular plants and fungi, we are lacking in nomenclators. Perhaps the test is: a pair: MEASURE_TAXONID_COMPLETENESS and an amendment LOOKUP_TAXONID, which could return a result state of ambiguous for homonyms.

[godfoder]

Related to #57

[ianengelbrecht]

Regarding "INTERNAL_PREREQUISITES_NOT_MET if all of the fields dwc:scientificName, dwc:subgenus, dwc:genus, dwc:family, dwc:order, dwc:class, dwc:phylum, dwc:kingdom are either not present or are EMPTY", would it make sense to say that only the ranks up to dwc:taxonRank are required? Also, would dwc:specificEpithet and dwc:infraspecificEpithet also be required where dwc:taxonRank is species or below? Also, can this be restricted to the primary taxon ranks, kingdom, phylum, class, order, family, genus, and have dwc:subgenus removed as an internal prerequisite. My apologies if these have already been discussed and resolved in the group.

[ArthurChapman]

Thanks @ianengelbrecht. What we are saying if none of those are present, or all that are present are empty, then the test can't be run. If some are present (even dwc:subGenus), then the test can be run (it may fail and be Non-Compliant if it can't be resolved). It not saying that all have to be present, but saying that the INTERNAL_PREREQUISITES can't be satisfied if there are no relevant fields or all are empty (all ... are not present). Perhaps we could rewrite to make it clearer (i.e. none of these fields are present) but we have tried to be consistent in the way we have worded all these. I've got this correct haven't I @chicoreus

[ianengelbrecht]

Thanks @ArthurChapman, how bout "INTERNAL_PREREQUISITES_NOT_MET if none of the fields dwc:scientificName, dwc:subgenus, dwc:genus, dwc:family, dwc:order, dwc:class, dwc:phylum, dwc:kingdom are present, or all of those present are EMPTY;"

[Tasilee]

Thanks @ianengelbrecht and @ArthurChapman. Unless I am mistaken (always possible), #105 covers that scenario.

[tucotuco]

@Tasilee Yes, issue #105 (TG2_TAXON_VALIDATION_EMPTY ) is a test to cover that situation, but this test (TG2_VALIDATION_TAXON_AMBIGUOUS) still needs a response for cases where the response from TG2_TAXON_VALIDATION_EMPTY is NON_COMPLIANT. How about the following wording?

INTERNAL_PREREQUISITES_NOT_MET if a) none of the fields dwc:scientificName, dwc:subgenus, dwc:genus, dwc:family, dwc:order, dwc:class, dwc:phylum, dwc:kingdom are present or b) all of those same fields that are present are EMPTY.

[Tasilee]

Thanks @tucotuco - I can live with that :). @ArthurChapman?

[ArthurChapman]

I think that is OK

[Tasilee]

Thanks @ArthurChapman. Done

[Tasilee]

Restructured Parameter(s) and Source authority

[ArthurChapman]

Replaces "#46" in notes with "VALIDATION_SCIENTIFICNAME_FOUND (4c09f127-737b-4686-82a0-7c8e30841590)"

[Tasilee]

One would hope that (all) the github issue references would be translated for the csv

[ArthurChapman]

It won't automatically translate and we need to add the GUID

[Tasilee]

A program like my Python code that I use for test spec dumps could easily do the translation (add Label and GUID) - and that creates a csv file.

[ArthurChapman]

Well - wherever it occurs in the GitHub table - it will need to be translated. I have been working through them whenever I find them.

[ArthurChapman]

Updated notes - changed "dwc:TaxonID" to "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]

Changed positive example (and test data that it was derived from) from

dwc:scientificName="Triplex rosarium Perry, 1811

to

dwc:scientificName="Triplex rosaria Perry, 1811

[Tasilee]

Splitting bdqffdq:Information Elements into "Information Elements ActedUpon" and "Information Elements Consulted": This one needs checking. My logic was from the Expected Response.

Also changed "Field" to "TestField", "Output Type" to "TestType" and updated "Specification Last Updated"

[Tasilee]

Changed all Information Elements to "ActedUpon" as per Paul's Java Code