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tdwg / bdq

Biodiversity Data Quality (BDQ) Interest Group
https://github.com/tdwg/bdq
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TG2-AMENDMENT_SEX_STANDARDIZED #284

Open ArthurChapman opened 7 months ago

ArthurChapman commented 7 months ago
TestField Value
GUID 33c45ae1-e2db-462a-a59e-7169bb01c5d6
Label AMENDMENT_SEX_STANDARDIZED
Description Proposes an amendment to the value of dwc:sex using the bdq:sourceAuthority.
TestType Amendment
Darwin Core Class dwc:Occurrence
Information Elements ActedUpon dwc:sex
Information Elements Consulted
Expected Response EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; INTERNAL PREREQUISITES_NOT_MET if dwc:sex is bdq:Empty; AMENDED the value of dwc:sex if it can be unambiguously matched to a term in the bdq:sourceAuthority; otherwise NOT_AMENDED
Data Quality Dimension Conformance
Term-Actions SEX_STANDARDIZED
Parameter(s) bdq:sourceAuthority
Source Authority bdq:sourceAuthority default = "GBIF Sex Vocabulary" [https://api.gbif.org/v1/vocabularies/Sex]} {"dwc:sex vocabulary API" [https://api.gbif.org/v1/vocabularies/Sex/concepts]}
Specification Last Updated 2024-03-25
Examples [dwc:sex="f": Response.status=AMENDED, Response.result=dwc:sex="Female", Response.comment="dwc:sex found in the bdq:sourceAuthority"]
[dwc:sex="x": Response.status=NOT_AMENDED, Response.result="", Response.comment="dwc:sex not found in the bdq:sourceAuthority"]
Source TG2
References
Example Implementations (Mechanisms)
Link to Specification Source Code
Notes For reference, a list of synonyms for dwc:sex values can be found at https://registry.gbif.org/vocabulary/Sex/concepts.
ymgan commented 7 months ago

I saw in #286

References: GBIF (2021). Darwin Core Nomenclatural Type Status Vocabulary http://rs.gbif.org/vocabulary/gbif/type_status

so should this also be in the References? https://rs.gbif.org/vocabulary/gbif/sex.xml

chicoreus commented 7 months ago

Noting that the current GBIF sex vocabulary is very animal centric.

ArthurChapman commented 7 months ago

Thanks @ymgan - added. @chicoreus - agreed

ymgan commented 6 months ago

oh, seems like GBIF is working on the vocabularies for sex at the moment https://github.com/gbif/vocabulary/issues/83

CecSve commented 6 months ago

@ymgan yes, we are updating vocabularies and moving them from enums to the vocabulary server, eventually. This is also the case for Type Status btw. The updates are to improve the mapping of hidden values provided by publishers. The sex vocabulary is very animal centric since most data comes from eBird @chicoreus - but please, if you know of any sources that cover concepts suitable for other groups, then we should be able to include them.

ArthurChapman commented 6 months ago

I have changed this to Immature/Incomplete pending the Vocabulary by GBIF.

CecSve commented 6 months ago

The vocabulary (v1) is now uploaded to the vocabulary server: https://registry.gbif.org/vocabulary/Sex and can be accessed by the vocabulary API (as Marie mentioned): https://techdocs.gbif.org/en/openapi/v1/vocabulary.

chicoreus commented 6 months ago

Grand. I've got an inquiry out with a botanist for sources for richer terms for some of the very complex botanical concepts around sex, but she hasn't gotten sources back yet.

ymgan commented 5 months ago

Similar to what @Tasilee mentioned in #277, #276, seems like GBIF API for Sex vocab is live https://api.gbif.org/v1/vocabularies/Sex/concepts

CecSve commented 5 months ago

This may not affect your decision but just wanted to highlight that the vocabularies (sex, geodeticdatum, kingdom, month, and taxonrank) are not yet used in interpretation in GBIF. We have to upload a couple more vocabularies before we initiate the process of reinterpretation for all occurrences.

Tasilee commented 5 months ago

Updated Source Authority to reflect new GBIF vocabulary. Does this imply this test could be CORE or Supplementary?

tucotuco commented 5 months ago

Updated Source Authority to reflect new GBIF vocabulary. Does this imply this test could be CORE or Supplementary?

I don't believe that where the vocabulary comes from is a criterion for CORE. It is a separate issue.

ArthurChapman commented 5 months ago

Changed to CORE following updating of GBIF Vocabulary, making a vocabulary available. This was the only reason it was made Immature/Incomplete earlier.

ArthurChapman commented 5 months ago

Note deleted as it referred to Supplementary test which no longer applies

Tasilee commented 5 months ago

Changed Source Authority from

bdq:sourceAuthority default = "Darwin Core sex" {[https://dwc.tdwg.org/list/#dwc_sex]} {dwc:sex vocabulary API [https://api.gbif.org/v1/vocabularies/Sex/concepts]}

to

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