diff --git a/frontend/public/schemas/20251121/linkml/manifest.json b/frontend/public/schemas/20251121/linkml/manifest.json index 8f7d7eebff..f1e1a531f1 100644 --- a/frontend/public/schemas/20251121/linkml/manifest.json +++ b/frontend/public/schemas/20251121/linkml/manifest.json @@ -1,5 +1,5 @@ { - "generated": "2026-01-20T11:48:39.141Z", + "generated": "2026-01-22T11:52:29.369Z", "schemaRoot": "/schemas/20251121/linkml", "totalFiles": 2969, "categoryCounts": { diff --git a/schemas/20251121/linkml/manifest.json b/schemas/20251121/linkml/manifest.json index f1e1a531f1..cc3efb0e9d 100644 --- a/schemas/20251121/linkml/manifest.json +++ b/schemas/20251121/linkml/manifest.json @@ -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": { diff --git a/schemas/20251121/linkml/modules/classes/Locality.yaml b/schemas/20251121/linkml/modules/classes/Locality.yaml new file mode 100644 index 0000000000..f9c4cf08fe --- /dev/null +++ b/schemas/20251121/linkml/modules/classes/Locality.yaml @@ -0,0 +1,188 @@ +# 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