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feat(schema): update generated timestamp in manifest and add Locality class with structured locality descriptions

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kempersc 2026-01-22 13:00:07 +01:00
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commit 367aaffc27
3 changed files with 190 additions and 2 deletions
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frontend/public/schemas/20251121/linkml/manifest.json
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{
"generated": "2026-01-20T11:48:39.141Z",
"generated": "2026-01-22T11:52:29.369Z",
"schemaRoot": "/schemas/20251121/linkml",
"totalFiles": 2969,
"categoryCounts": {

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schemas/20251121/linkml/manifest.json
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@ -1,5 +1,5 @@
{
"generated": "2026-01-22T11:52:29.369Z",
"generated": "2026-01-22T12:00:07.511Z",
"schemaRoot": "/schemas/20251121/linkml",
"totalFiles": 2969,
"categoryCounts": {

188
schemas/20251121/linkml/modules/classes/Locality.yaml Normal file
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# Locality class
# Structured representation of locality/place descriptions for biological specimens.
#
# MIGRATION NOTE (2026-01-19):
# Created as part of collection_locality_text migration per slot_fixes.yaml (Rule 53).
#
# Darwin Core alignment: Captures dwc:verbatimLocality with structured provenance.
id: https://nde.nl/ontology/hc/class/Locality
name: Locality
title: Locality Class
prefixes:
linkml: https://w3id.org/linkml/
hc: https://nde.nl/ontology/hc/
schema: http://schema.org/
crm: http://www.cidoc-crm.org/cidoc-crm/
dcterms: http://purl.org/dc/terms/
dwc: http://rs.tdwg.org/dwc/terms/
skos: http://www.w3.org/2004/02/skos/core#
imports:
- linkml:types
- ../metadata
- ../slots/has_or_had_label
- ../slots/has_or_had_note
- ../slots/has_or_had_provenance
- ../slots/language
default_prefix: hc
classes:
Locality:
class_uri: dcterms:Location
description: >-
Structured locality description for specimens and collection events.
**Purpose**:
Captures verbatim locality text as recorded on specimen labels or in field notes,
preserving the original description for historical accuracy while allowing
structured interpretation.
**Darwin Core Alignment**:
- `verbatim_text` → dwc:verbatimLocality
- Preserves original text exactly as recorded
- Supports historical specimens with non-standard descriptions
**TEMPORAL SEMANTICS**:
Locality descriptions may vary over time:
- Original label text (historical)
- Interpreted/standardized descriptions (current)
- Multiple descriptions from different sources
**Example**:
```yaml
Locality:
verbatim_text: "Mauritius, near Port Louis, in forest"
original_language: "en"
has_or_had_provenance:
data_source: "specimen_label"
extraction_date: "2025-01-19"
```
**REPLACES**:
- Simple `collection_locality_text` string slot
- Adds structured provenance and language tracking
exact_mappings:
- dcterms:Location
close_mappings:
- dwc:Location
- schema:Place
related_mappings:
- crm:E53_Place
mixins:
- HasProvenance
slots:
- has_or_had_label
- has_or_had_note
- has_or_had_provenance
- language
attributes:
verbatim_text:
description: >-
Verbatim locality description exactly as recorded on label or in field notes.
Preserves original text including spelling, abbreviations, and formatting.
range: string
required: true
slot_uri: dwc:verbatimLocality
examples:
- value: "Mauritius, near Port Louis, in forest"
- value: "Indonesia: Java: Mt. Gede, 1500m"
- value: "Argentina, Buenos Aires Province"
- value: "Nr. Cape Town, on rocks by sea"
original_language:
description: >-
ISO 639-1 language code of the original locality text.
range: string
slot_uri: dcterms:language
examples:
- value: "en"
- value: "nl"
- value: "la"
description: Latin (common in historical specimens)
interpretation_notes:
description: >-
Notes on interpretation of historical or ambiguous locality text.
range: string
slot_uri: skos:note
examples:
- value: "Port Louis refers to the capital of Mauritius"
- value: "Mt. Gede is Gunung Gede, elevation approximately 1500m"
slot_usage:
has_or_had_label:
description: >-
Standardized or interpreted locality name.
Use when verbatim text has been parsed into standard form.
range: string
examples:
- value: "Port Louis, Mauritius"
has_or_had_note:
description: >-
Additional notes about this locality record.
range: string
has_or_had_provenance:
description: >-
Provenance of this locality description.
Tracks source (label, field notes, database) and extraction details.
range: ProvenanceBlock
inlined: true
comments:
- Created 2026-01-19 from collection_locality_text migration (Rule 53)
- Aligns with Darwin Core dwc:verbatimLocality
- Preserves original text while allowing structured interpretation
- Supports historical specimens with non-standard locality descriptions
see_also:
- https://dwc.tdwg.org/terms/#dwc:verbatimLocality
- https://dwc.tdwg.org/terms/#dwc:Location
annotations:
custodian_types: '["B", "M", "R"]'
custodian_types_rationale: >-
Primarily used for Botanical/Zoo (B), Museum (M), and Research (R) custodians
with biological specimen collections.
custodian_types_primary: "B"
specificity_score: "0.65"
specificity_rationale: >-
Moderately specific - primarily for natural history specimens.
template_specificity:
museum_search: "0.70"
collection_discovery: "0.75"
general_heritage: "0.50"
examples:
- value:
verbatim_text: "Mauritius, near Port Louis, in forest"
original_language: "en"
has_or_had_label: "Port Louis, Mauritius"
has_or_had_provenance:
data_source: "specimen_label"
extraction_date: "2025-01-19"
description: Locality for historical Dodo specimen
- value:
verbatim_text: "Indonesia: Java: Mt. Gede, 1500m"
original_language: "en"
interpretation_notes: "Mt. Gede is Gunung Gede volcano in West Java"
has_or_had_label: "Gunung Gede, West Java, Indonesia"
description: Indonesian specimen with elevation data
- value:
verbatim_text: "Prope Cape Town, in rupibus ad mare"
original_language: "la"
interpretation_notes: "Latin: 'Near Cape Town, on rocks by the sea'"
has_or_had_label: "Cape Town coastline, South Africa"
description: Historical specimen with Latin locality description