1516d509cf
- Added `id`, `name`, `title`, and `description` fields to multiple LinkML class YAML files. - Standardized prefixes across all class definitions. - Introduced a new script `fix_linkml_metadata.py` to automate the addition of metadata to class files. - Updated existing class files to ensure compliance with the new metadata structure.
198 lines
6.4 KiB
YAML
198 lines
6.4 KiB
YAML
id: https://nde.nl/ontology/hc/class/Locality
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name: Locality
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title: Locality
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description: LinkML class definition for Locality
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prefixes:
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linkml: https://w3id.org/linkml/
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schema: http://schema.org/
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skos: http://www.w3.org/2004/02/skos/core#
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rico: https://www.ica.org/standards/RiC/ontology#
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wd: http://www.wikidata.org/entity/
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# Locality class
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# Structured representation of locality/place descriptions for biological specimens.
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#
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# MIGRATION NOTE (2026-01-19):
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# Created as part of collection_locality_text migration per slot_fixes.yaml (Rule 53).
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#
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# Darwin Core alignment: Captures dwc:verbatimLocality with structured provenance.
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id: https://nde.nl/ontology/hc/class/Locality
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name: Locality
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title: Locality Class
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prefixes:
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linkml: https://w3id.org/linkml/
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hc: https://nde.nl/ontology/hc/
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schema: http://schema.org/
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crm: http://www.cidoc-crm.org/cidoc-crm/
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dcterms: http://purl.org/dc/terms/
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dwc: http://rs.tdwg.org/dwc/terms/
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skos: http://www.w3.org/2004/02/skos/core#
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imports:
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- linkml:types
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- ../metadata
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- ../slots/has_or_had_label
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- ../slots/has_or_had_note
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- ../slots/has_or_had_provenance
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- ../slots/language
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default_prefix: hc
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classes:
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Locality:
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class_uri: dcterms:Location
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description: >-
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Structured locality description for specimens and collection events.
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**Purpose**:
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Captures verbatim locality text as recorded on specimen labels or in field notes,
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preserving the original description for historical accuracy while allowing
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structured interpretation.
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**Darwin Core Alignment**:
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- `verbatim_text` → dwc:verbatimLocality
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- Preserves original text exactly as recorded
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- Supports historical specimens with non-standard descriptions
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**TEMPORAL SEMANTICS**:
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Locality descriptions may vary over time:
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- Original label text (historical)
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- Interpreted/standardized descriptions (current)
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- Multiple descriptions from different sources
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**Example**:
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```yaml
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Locality:
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verbatim_text: "Mauritius, near Port Louis, in forest"
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original_language: "en"
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has_or_had_provenance:
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data_source: "specimen_label"
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extraction_date: "2025-01-19"
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```
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**REPLACES**:
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- Simple `collection_locality_text` string slot
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- Adds structured provenance and language tracking
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exact_mappings:
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- dcterms:Location
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close_mappings:
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- dwc:Location
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- schema:Place
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related_mappings:
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- crm:E53_Place
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mixins:
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- HasProvenance
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slots:
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- has_or_had_label
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- has_or_had_note
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- has_or_had_provenance
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- language
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attributes:
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verbatim_text:
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description: >-
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Verbatim locality description exactly as recorded on label or in field notes.
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Preserves original text including spelling, abbreviations, and formatting.
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range: string
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required: true
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slot_uri: dwc:verbatimLocality
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examples:
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- value: "Mauritius, near Port Louis, in forest"
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- value: "Indonesia: Java: Mt. Gede, 1500m"
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- value: "Argentina, Buenos Aires Province"
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- value: "Nr. Cape Town, on rocks by sea"
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original_language:
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description: >-
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ISO 639-1 language code of the original locality text.
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range: string
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slot_uri: dcterms:language
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examples:
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- value: "en"
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- value: "nl"
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- value: "la"
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description: Latin (common in historical specimens)
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interpretation_notes:
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description: >-
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Notes on interpretation of historical or ambiguous locality text.
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range: string
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slot_uri: skos:note
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examples:
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- value: "Port Louis refers to the capital of Mauritius"
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- value: "Mt. Gede is Gunung Gede, elevation approximately 1500m"
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slot_usage:
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has_or_had_label:
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description: >-
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Standardized or interpreted locality name.
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Use when verbatim text has been parsed into standard form.
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range: string
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examples:
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- value: "Port Louis, Mauritius"
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has_or_had_note:
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description: >-
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Additional notes about this locality record.
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range: string
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has_or_had_provenance:
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description: >-
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Provenance of this locality description.
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Tracks source (label, field notes, database) and extraction details.
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range: ProvenanceBlock
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inlined: true
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comments:
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- Created 2026-01-19 from collection_locality_text migration (Rule 53)
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- Aligns with Darwin Core dwc:verbatimLocality
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- Preserves original text while allowing structured interpretation
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- Supports historical specimens with non-standard locality descriptions
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see_also:
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- https://dwc.tdwg.org/terms/#dwc:verbatimLocality
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- https://dwc.tdwg.org/terms/#dwc:Location
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annotations:
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custodian_types: '["B", "M", "R"]'
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custodian_types_rationale: >-
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Primarily used for Botanical/Zoo (B), Museum (M), and Research (R) custodians
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with biological specimen collections.
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custodian_types_primary: "B"
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specificity_score: "0.65"
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specificity_rationale: >-
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Moderately specific - primarily for natural history specimens.
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template_specificity:
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museum_search: "0.70"
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collection_discovery: "0.75"
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general_heritage: "0.50"
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examples:
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- value:
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verbatim_text: "Mauritius, near Port Louis, in forest"
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original_language: "en"
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has_or_had_label: "Port Louis, Mauritius"
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has_or_had_provenance:
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data_source: "specimen_label"
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extraction_date: "2025-01-19"
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description: Locality for historical Dodo specimen
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- value:
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verbatim_text: "Indonesia: Java: Mt. Gede, 1500m"
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original_language: "en"
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interpretation_notes: "Mt. Gede is Gunung Gede volcano in West Java"
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has_or_had_label: "Gunung Gede, West Java, Indonesia"
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description: Indonesian specimen with elevation data
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- value:
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verbatim_text: "Prope Cape Town, in rupibus ad mare"
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original_language: "la"
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interpretation_notes: "Latin: 'Near Cape Town, on rocks by the sea'"
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has_or_had_label: "Cape Town coastline, South Africa"
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description: Historical specimen with Latin locality description
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