fc405445c6
- Removed obsolete slots: `has_or_had_custodian_observation`, `provider`, and `specificity_annotation`. - Updated `has_or_had_score` slot to use `SpecificityScore` class and modified its description and examples. - Added new slots: `end_seconds`, `end_time`, `has_archive_path`, `has_or_had_custodian_name`, `protocol_name`, and `protocol_version`. - Introduced a script `check_annotation_types.py` to validate the presence and structure of `custodian_types` in YAML files. - Added a script `update_specificity.py` to automate updates related to `SpecificityAnnotation` to `SpecificityScore`.
44 lines
2.1 KiB
YAML
44 lines
2.1 KiB
YAML
id: https://nde.nl/ontology/hc/class/BOLDIdentifier
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name: bold_identifier_class
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title: BOLD Identifier Class
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description: Barcode of Life Data System (BOLD) identifier for biological specimens. Links heritage biological objects to
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their DNA barcode records in BOLD.
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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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dcterms: http://purl.org/dc/terms/
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schema: http://schema.org/
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default_prefix: hc
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imports:
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- linkml:types
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- ../slots/has_or_had_description
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- ../slots/has_or_had_score
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classes:
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BOLDIdentifier:
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class_uri: schema:PropertyValue
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description: 'A Barcode of Life Data System (BOLD) identifier linking a biological specimen to its DNA barcode record.
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**WHAT IS BOLD?** BOLD (Barcode of Life Data System) is an online workbench and database for DNA barcoding. It stores
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specimen data and DNA barcode sequences, enabling species identification through DNA. **USE CASES**: 1. **Specimen Identification**:
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Link natural history specimens to DNA data 2. **Species Verification**: Cross-reference morphological IDs with DNA barcodes
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3. **Research Provenance**: Document genetic sampling of collection objects **IDENTIFIER FORMAT**: BOLD identifiers
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follow the pattern: BOLD:XXXNNN - Process IDs: BOLD:AAA0001 - Sample IDs: Institution-specific prefixes **EXTERNAL LINKS**:
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- BOLD Systems: https://boldsystems.org/ - Record URL pattern: https://boldsystems.org/index.php/Public_RecordView?processid={id}'
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exact_mappings:
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- schema:PropertyValue
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close_mappings:
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- dcterms:identifier
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slots:
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- has_or_had_description
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- has_or_had_score
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comments:
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- Used for DNA barcode identifiers in natural history collections
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- Links physical specimens to molecular data
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- Part of global biodiversity identification infrastructure
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examples:
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- value:
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id: https://nde.nl/ontology/hc/bold-id/NLNAT001-21
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identifier_url: https://boldsystems.org/index.php/Public_RecordView?processid=NLNAT001-21
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annotations:
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specificity_score: 0.1
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specificity_rationale: Generic utility class/slot created during migration
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custodian_types: '[''*'']'
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