TG2-AMENDMENT_TAXONRANK_STANDARDIZED #163

ArthurChapman · 2018-09-03T04:51:37Z

TestField	Value
GUID	e39098df-ef46-464c-9aef-bcdeee2a88cb
Label	AMENDMENT_TAXONRANK_STANDARDIZED
Description	Proposes an amendment to the value of dwc:taxonRank using the bdq:sourceAuthority.
TestType	Amendment
Darwin Core Class	dwc:Taxon
Information Elements ActedUpon	dwc:taxonRank
Information Elements Consulted
Expected Response	EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; INTERNAL PREREQUISITES_NOT_MET if dwc:taxonRank is bdq:Empty; AMENDED the value of dwc:taxonRank if it can be unambiguously matched to a term in the bdq:sourceAuthority; otherwise NOT_AMENDED
Data Quality Dimension	Conformance
Term-Actions	TAXONRANK_STANDARDIZED
Parameter(s)	bdq:sourceAuthority
Source Authority	bdq:sourceAuthority default = "GBIF TaxonRank Vocabulary" [https://api.gbif.org/v1/vocabularies/TaxonRank]} {"dwc:taxonRank vocabulary API" [https://api.gbif.org/v1/vocabularies/TaxonRank/concepts]}}
Specification Last Updated	2023-09-18
Examples	[dwc:taxonRank="sp.": Response.status=AMENDED, Response.result=dwc:taxonRank="species", Response.comment="dwc:taxonRank contains an interpretable value in the bdq:sourceAuthority"]
	[dwc:taxonRank="sic.": Response.status=NOT_AMENDED, Response.result="", Response.comment="dwc:taxonRank does not contain an interpretable value in the bdq:sourceAuthority"]
Source	TDWG2018
References	GBIF Registry (2023) GBIF Vocabulary: Taxonomic Rank. https://registry.gbif.org/vocabulary/TaxonRank/concepts
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#L2276
Notes	For reference, information about possible values of dwc:taxonRank can be found at https://registry.gbif.org/vocabulary/TaxonRank/concepts

chicoreus · 2018-09-07T15:54:50Z

Added guid.

chicoreus · 2019-09-06T19:15:01Z

I'd be a little bit hesitant to recommend the GBIF rank vocabulary, it is zoologically centric (there is no entry for Division, and translations of Division are mapped onto phylum, which is at the same level but isn't the same rank), most of the obscure infrasubspecific ranks found in botany are absent (particularly lusus and prolus), virological realm and subrealm are missing, etc.

tucotuco · 2019-09-06T19:21:19Z

One could get propose the required changes to the GBIF vocabulary. I suspect paleo would have something to say about what is there as well.

ArthurChapman · 2019-09-06T21:36:20Z

I agree with @tucotuco - best is to propose some changes to GBIF's vocabulary. I am sure they would be receptive. There is no good alternative that covers everything so comprehensively. Incidentally, lusus and prolus are not formal ranks under the International Code of Algae, Fungi and Plants

Tasilee · 2019-09-08T22:18:59Z

@tucotuco - I also support the suggestion, and agree with @ArthurChapman that GBIF should be supportive

Tasilee · 2020-04-01T04:36:47Z

All: This is a random test to demo my updates to the table fields Parameter(s), References (in this case removed as there is no additional reference/s beyond the xml end point defined in Notes) and Notes is a draft template of what we agreed. Please check and thumbs or otherwise.

ArthurChapman · 2020-04-01T05:36:37Z

Looks OK - but in that case - that is a good reference - only other references would be to the Codes of Nomenclature and I'd prefer not to go there. Eventually, the default may be to an API, in which case you would want to retain the reference to the human readable vocabulary.

Tasilee · 2021-10-25T00:20:40Z

Corrected example: dwc:taxonRecord="sp." becomes dwc:taxonRank="Species" to
dwc:taxonRank="sp." becomes dwc:taxonRank="Species"

ArthurChapman · 2022-03-20T22:19:42Z

I have attempted my first addition of a Definition

| Definition | An Amendment of the value in Taxon Rank to conform with the value obtained from a Paramaterized Source Authority. If no parameter is set, the source authority defaults to the latest Taxonomic Rank GBIF Vocabulary. |

ArthurChapman · 2022-03-20T23:01:04Z

Question. Is it OK here to use "Taxon Rank" in the definition - or should it be "dwc:taxonRank. I was trying to go towards plain English, but this may not work in all cases.

e.g.
| Definition | An Amendment of the value in Taxon Rank to conform with the value obtained from a Paramaterized Source Authority. If no parameter is set, the source authority defaults to the latest Taxonomic Rank GBIF Vocabulary. |
OR
| Definition | An Amendment of the value in dwc:taxonRank to conform with the value obtained from a Paramaterized Source Authority. If no parameter is set, the source authority defaults to the latest Taxonomic Rank GBIF Vocabulary. |

Tasilee · 2022-03-23T06:32:20Z

I am not convinced of the need for “Brief”. If we can’t succinctly describe it in “Description”, we fail. Why have ‘two bites at the cherry’ when one will do. Ocham’s Razor.

tucotuco · 2022-03-23T13:04:53Z

@ArthurChapman I still think think that the description should not have the "single record" part in it, but I am willing to not fight it to move forward.

Tasilee · 2022-03-23T21:27:19Z

IF (and to me it is a big if) 'Single record' is REQUIRED for conformance with the Framework, then surely it should be a part of the specifications - as we had it previously (as "Resource Type"). We found that all the 'tests' were "single record" so we removed it.

chicoreus · 2022-03-23T21:49:03Z

@Tasilee

Consider the following RDF:

<rdf:Description rdf:about="urn:uuid:e39098df-ef46-464c-9aef-bcdeee2a88cb">
    <rdf:type rdf:resource="http://rs.tdwg.org/ffdq#Specification"/>
    <rdfs:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; AMENDED if the value of dwc:taxonRank was standardized using the bdq:sourceAuthority; otherwise NOT_AMENDED</rdfs:description>
    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AMENDMENT_TAXONRANK_STANDARDIZED</rdfs:label>
</rdf:Description>

<rdf:Description rdf:about="urn:uuid:f559e3a3-c756-44f2-a9c6-555d59c3535e">
    <hasSpecification xmlns="http://rs.tdwg.org/ffdq#" rdf:resource="urn:uuid:e39098df-ef46-464c-9aef-bcdeee2a88cb"/>
    <implementedBy xmlns="http://rs.tdwg.org/ffdq#" rdf:resource="urn:uuid:919e8e12-808c-46ca-81af-d90bdbf5321c"/>
    <rdf:type rdf:resource="http://rs.tdwg.org/ffdq#Implementation"/>
</rdf:Description>

<rdf:Description rdf:about="urn:uuid:2d81389a-ffe5-479a-a7d6-7a131f553b36">
    <enhancementInContext xmlns="http://rs.tdwg.org/ffdq#" rdf:resource="urn:uuid:5c1b9090-af8c-4b8c-b77a-0c8de69ba690"/>
    <hasSpecification xmlns="http://rs.tdwg.org/ffdq#" rdf:resource="urn:uuid:e39098df-ef46-464c-9aef-bcdeee2a88cb"/>
    <rdf:type rdf:resource="http://rs.tdwg.org/ffdq#AmendmentMethod"/>
</rdf:Description>

<rdf:Description rdf:about="urn:uuid:5c1b9090-af8c-4b8c-b77a-0c8de69ba690">
    <hasEnhancement xmlns="http://rs.tdwg.org/ffdq#" rdf:resource="urn:uuid:d1c371b0-87af-4fda-bde8-3f22f1abc745"/>
    <hasInformationElement xmlns="http://rs.tdwg.org/ffdq#" rdf:resource="urn:uuid:9e1b5503-2ef5-4663-8d42-8ae66355389c"/>
    <hasResourceType xmlns="http://rs.tdwg.org/ffdq#" rdf:resource="rt:SingleRecord"/>
    <rdf:type rdf:resource="http://rs.tdwg.org/ffdq#ContextualizedEnhancement"/>
    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Description needed here</rdfs:label>
</rdf:Description>

<rdf:Description rdf:about="urn:uuid:9e1b5503-2ef5-4663-8d42-8ae66355389c">
    <composedOf xmlns="http://rs.tdwg.org/ffdq#" rdf:resource="http://rs.tdwg.org/dwc/terms/taxonRank"/>
    <rdf:type rdf:resource="http://rs.tdwg.org/ffdq#InformationElement"/>
</rdf:Description>

<rdf:Description rdf:about="urn:uuid:d1c371b0-87af-4fda-bde8-3f22f1abc745">
    <rdf:type rdf:resource="http://rs.tdwg.org/ffdq#Enhancement"/>
    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Conformance: standardized</rdfs:label>
</rdf:Description>

I'm seeing a need for a label on the ContextualizedEnhancement, where the text "Description needed here" is.

Tasilee · 2022-03-23T23:27:59Z

Why not "Description needed here" -> "Single record"? :)

Tasilee · 2022-03-27T21:13:37Z

Looking to conform the Expected Response of AMENDMENTs to "AMEND {target} if ...", this one could become 'trivial':

EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; AMEND dwc:taxonRank using bdq:sourceAuthority; otherwise NOT_AMENDED

We do have the precursor #161 and #162 but we also agreed that the 'tests' should be stand-alone. Maybe the ER should be something like

EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; AMEND the value of dwc:taxonRank if this value can be matched to a standard value in bdq:sourceAuthority; otherwise NOT_AMENDED

?

ArthurChapman · 2022-03-27T21:19:50Z

Note that we have used AMENDED everywhere - not AMEND and fits with NOT_AMENDED

Agree to your change - I checked all the Descriptions so that we said "value of"

…andardized. DESCRIPTION: Minimal implmementation using hardcoded copy of current values able to match on differences in case and a few alternative text forms. Needs lookup and cache implementation and darwin cloud implementation. Working minimal implementation including unit test.

Tasilee · 2022-09-09T01:46:18Z

Done

chicoreus · 2022-12-11T21:19:59Z

Proposal from discussion on 2022-12-11: Concern, what to do when the value is "especie", or another synonym or language variant in the specified vocabulary, expectation of amend to standard term would be that this would be that this value would be amended to "species", the standard term in the vocabulary. This could be undesirable for some users who wish to use a particular language variant for their data. Thus, similar to our handling of different national standards for geodeticDatum, proposal would be for a parameter for this, and for other amendments that conform data to a vocabulary where the parameter would allow one of three cases: (1) The amendment propose the standard term in the vocabulary, using language variants and synonyms in the vocabulary as values to be amended to the standard form, or (2) The amendment propose a particular (specified) language variant of the vocabulary term, e.g. converting all values in taxonRank to a spanish form, or (3), treating any synonym or language variant in the vocabulary as valid, and only attempting (if possible) to conform values to the vocabulary if they don't occur anywhere within it (e.g. conforming case, SPECIES to species, and ESPECIE to especie),

chicoreus · 2023-01-30T14:23:22Z

Per note by @timrobertson100 in #170 we should probably switch the Source Authority to the more current, complete, and comprehensive one at https://registry.gbif.org/vocabulary/TaxonRank/concepts (available in machine readable form at https://api.gbif.org/v1/vocabularies/TaxonRank/concepts ). Likewise, we should make a similar change in #162

ArthurChapman · 2023-02-13T22:25:23Z

Updated "Source Authority" and "References" in accord with @chicoreus comment above. @Tasilee to check.

Tasilee · 2023-02-26T22:32:15Z

Thanks @ArthurChapman: Checked.

Tasilee · 2023-03-01T20:45:46Z

Could I suggest we replace the Expected response

EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; AMENDED the value of dwc:taxonRank if this value can be matched to a standard value in bdq:sourceAuthority; otherwise NOT_AMENDED

with

EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; AMENDED the value of dwc:taxonRank if it can be unambiguously matched to a term in bdq:sourceAuthority; otherwise NOT_AMENDED

?

Tasilee · 2023-03-01T20:50:21Z

Is it odd that the Expected Response doesn't contain an INTERNAL_PREREQUISITES_NOT_MET? Should we have something like

EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; INTERNAL PREREQUISITES_NOT_MET if dwc:taxonRank is EMPTY; AMENDED the value of dwc:taxonRank if it can be unambiguously matched to a term in bdq:sourceAuthority; otherwise NOT_AMENDED

?

ArthurChapman · 2023-03-01T21:55:08Z

That would make sense to me for consistency, but without it - it still works.

Tasilee · 2023-03-02T05:14:59Z

The determining factor is whether it is more appropriate to return INTERNAL PREREQUISITES_NOT_MET or NOT_AMENDED if dwc:taxonRank is EMPTY.

tucotuco · 2023-03-11T02:39:37Z

I would prefer returning INTERNAL PREREQUISITES_NOT_MET. It tells you better where the test failed, not just that it did.

Tasilee · 2023-03-19T21:07:59Z

OK, then I have edited the Expected Response

EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; AMENDED the value of dwc:taxonRank if this value can be unambiguously matched to a value in bdq:sourceAuthority; otherwise NOT_AMENDED

to

EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; INTERNAL PREREQUISITES_NOT_MET if dwc:taxonRank is EMPTY; AMENDED the value of dwc:taxonRank if it can be unambiguously matched to a term in bdq:sourceAuthority; otherwise NOT_AMENDED

Tasilee · 2023-06-13T01:15:08Z

Restructured Parameter(s) and Source authority

Tasilee · 2023-07-11T01:21:24Z

Post Zoom 11/7/2023, I have aligned the Source Authority with the suggested syntax:

bdq:sourceAuthority default = "GBIF Vocabulary: Taxonomic Rank" [https://api.gbif.org/v1/vocabularies/TaxonRank/concepts]

to

bdq:sourceAuthority default = "Darwin Core" {https://dwc.tdwg.org} {dwc:taxonRank [https://dwc.tdwg.org/list/#dwc_taxonRank]} {GBIF Vocabulary: Taxonomic Rank [https://api.gbif.org/v1/vocabularies/TaxonRank/concepts]}

chicoreus · 2023-07-11T01:27:34Z

On Mon, 10 Jul 2023 18:21:34 -0700 Lee Belbin ***@***.***> wrote: Post Zoom 11/7/2023, I have aligned the Source Authority with the suggested syntax: bdq:sourceAuthority default = "GBIF Vocabulary: Taxonomic Rank" [https://api.gbif.org/v1/vocabularies/TaxonRank/concepts]

This is probably a case where we do want to assert that the GBIF Vocabulary is the source authority, as it provides a controled vocabulary, while Darwin Core does not.

Tasilee · 2023-07-11T21:14:41Z

From @chicoreus's comment (#162 (comment)), changed Source Authority from

bdq:sourceAuthority default = "Darwin Core" {https://dwc.tdwg.org} {dwc:taxonRank [https://dwc.tdwg.org/list/#dwc_taxonRank]} {GBIF Vocabulary: Taxonomic Rank [https://api.gbif.org/v1/vocabularies/TaxonRank/concepts]}

to

bdq:sourceAuthority default = "GBIF Vocabulary: Taxonomic Rank" {[https://api.gbif.org/v1/vocabularies/TaxonRank/concepts]} {dwc:taxonRank [https://dwc.tdwg.org/list/#dwc_taxonRank]}

…pecifications. Addressed tdwg/bdq#163 AMENDMENT_TAXONRANK_STANDARDIZED Updated metadata, ProvidesVersion and Specification annotations. Removed reviewed stub method.

…pecifications. Fix for tdwg/bdq#163 AMENDMENT_TAXONRANK_STANDARDIZED not providing correct response when taxonRank is empty.

Tasilee · 2023-09-18T05:29:14Z

Splitting bdqffdq:Information Elements into "Information Elements ActedUpon" and "Information Elements Consulted".

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

Tasilee · 2024-04-16T03:08:53Z

Changed Source Authority from

bdq:sourceAuthority default = "GBIF Vocabulary: Taxonomic Rank" {[https://api.gbif.org/v1/vocabularies/TaxonRank/concepts]} {dwc:taxonRank [https://dwc.tdwg.org/list/#dwc_taxonRank]}

to

bdq:sourceAuthority default = "GBIF TaxonRank Vocabulary" [https://api.gbif.org/v1/vocabularies/TaxonRank]} {"dwc:taxonRank vocabulary API" [https://api.gbif.org/v1/vocabularies/TaxonRank/concepts]}

ArthurChapman added TG2 Amendment NAME Conformance VOCABULARY labels Sep 3, 2018

Tasilee changed the title ~~TG2-AMENDMENT_TAXONRANK_STANDARDIZED~~ TG2 - AMENDMENT_TAXONRANK_STANDARDIZED Sep 4, 2018

Tasilee mentioned this issue Sep 5, 2018

TaxonRank #159

Closed

Tasilee added Test Test Tests created by TG2, either CORE, Supplementary or DO NOT IMPLEMENT and removed Test labels Sep 25, 2018

This was referenced Sep 26, 2018

TG4 - Vocabularies needed for the Tests and Assertions #172

Open

TG4 - taxonRank #170

Open

ArthurChapman added the responseDone label Oct 31, 2018

Tasilee removed the responseDone label Nov 5, 2018

tucotuco added the Parameterized Test requires a parameter label Nov 5, 2018

Tasilee mentioned this issue May 16, 2019

TG2 - Parameterized #178

Closed

Tasilee changed the title ~~TG2 - AMENDMENT_TAXONRANK_STANDARDIZED~~ TG2-AMENDMENT_TAXONRANK_STANDARDIZED Jun 5, 2019

Tasilee mentioned this issue Apr 1, 2020

TG2-Create a file containing non normative parameter default values for relevant tests #182

Open

Tasilee mentioned this issue Apr 13, 2020

TG2-AMENDMENT_[]_STANDARDIZED source authorities #185

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ArthurChapman mentioned this issue Mar 23, 2022

TG2 - Structuring Test Descriptions #197

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Tasilee mentioned this issue Mar 19, 2023

TG2-AMENDMENT_SCIENTIFICNAME_FROM_SCIENTIFICNAMEID #71

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TG2-AMENDMENT_TAXONRANK_STANDARDIZED #163

TG2-AMENDMENT_TAXONRANK_STANDARDIZED #163

ArthurChapman commented Sep 3, 2018 •

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TG2-AMENDMENT_TAXONRANK_STANDARDIZED #163

TG2-AMENDMENT_TAXONRANK_STANDARDIZED #163

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