DiSSCo Digital Specimen v0.4

DiSSCo (Distributed System of Scientific Collections) is a European research infrastructure for natural science collections. The DiSSCo Digital Specimen specification defines a FAIR Digital Object (FDO) format for representing physical specimens in natural science collections as machine-actionable digital objects.

The specification builds on Darwin Core vocabulary while adding DiSSCo-specific extensions for collection management, persistent identifiers, and FAIR compliance. Each Digital Specimen is assigned a DOI and includes MIDS (Minimum Information about a Digital Specimen) level indicators.

flowchart TB
    subgraph core["Core"]
        DS[DigitalSpecimen]
        ID[Identification]
        TI[TaxonIdentification]
    end

    subgraph event["Collection Event"]
        EVT[Event]
        LOC[Location]
        GEO[Georeference]
    end

    subgraph agents["Agents"]
        AGT[Agent]
        ROL[AgentRole]
    end

    subgraph metadata["Metadata"]
        AST[Assertion]
        CIT[Citation]
        IDN[Identifier]
        ER[EntityRelationship]
    end

    subgraph extensions["Extensions"]
        SP[SpecimenPart]
        CA[ChronometricAge]
        TM[TombstoneMetadata]
    end

    %% Core relationships
    DS --> ID
    DS --> EVT
    DS --> AGT
    DS --> AST
    DS --> CIT
    DS --> IDN
    DS --> ER
    DS --> SP
    DS --> CA
    DS --> TM

    %% Nested relationships
    ID --> TI
    ID --> AGT
    ID --> CIT
    EVT --> LOC
    EVT --> AGT
    LOC --> GEO
    AGT --> ROL
    AGT --> IDN
    AST --> AGT
    AST --> CIT

    classDef core fill:#e8f5e9,stroke:#4caf50,stroke-width:2px
    classDef event fill:#fff3e0,stroke:#ff9800,stroke-width:2px
    classDef agent fill:#e3f2fd,stroke:#2196f3,stroke-width:2px
    classDef meta fill:#fce4ec,stroke:#e91e63,stroke-width:2px
    classDef ext fill:#f3e5f5,stroke:#9c27b0,stroke-width:2px

    class DS,ID,TI core
    class EVT,LOC,GEO event
    class AGT,ROL agent
    class AST,CIT,IDN,ER meta
    class SP,CA,TM ext

Entities

Category	Entities
Core	DigitalSpecimen, Identification, TaxonIdentification
Collection Event	Event, Location, Georeference
Agents	Agent, AgentRole
Metadata	Assertion, Citation, Identifier, EntityRelationship
Extensions	SpecimenPart, ChronometricAge, TombstoneMetadata

Key Concepts

FAIR Digital Objects: Each Digital Specimen is a FAIR Digital Object with a DOI identifier, making it globally unique, persistent, and resolvable. The FDO approach ensures specimens are findable, accessible, interoperable, and reusable.

MIDS Levels: The Minimum Information about a Digital Specimen (MIDS) framework defines data quality levels from 0-3:

• MIDS 0: Digital object exists with basic identifier
• MIDS 1: Basic metadata (collection, taxon, geography)
• MIDS 2: Extended metadata (coordinates, media links)
• MIDS 3: Full metadata including images and detailed provenance

Organisation Identifiers: DiSSCo requires organisation identifiers in ROR or Wikidata format, enabling unambiguous linking to collection-holding institutions.

Topic Classification: Specimens are classified by:

• topicOrigin: Natural, Human-made, Mixed origin
• topicDomain: Life, Environment, Earth System, Extraterrestrial
• topicDiscipline: Botany, Zoology, Geology, Palaeontology, etc.

Agent Roles: People and organisations are represented as Agent entities with typed roles (collector, identifier, creator). Agents can have ORCID identifiers for researchers or ROR identifiers for institutions.

Validation Rules

The DiSSCo profile includes validation rules for:

• DOI format for specimen identifiers (^https://doi\.org/.*$)
• ROR or Wikidata format for organisation identifiers
• MIDS level range (0-3)
• Scientific name required for TaxonIdentification

Use Cases

• Collection digitization: Creating digital representations of physical specimens
• Data aggregation: European-wide specimen data infrastructure
• Linked data: Connecting specimens to publications, sequences, images
• Specimen loans: Digital tracking of physical specimen movements
• Biodiversity research: FAIR access to collection data for research

Entity-Relationship Diagram

erDiagram
    DigitalSpecimen {
        string id PK
        string type
        string identifier
        integer version
        string status
        datetime created
        datetime modified
        integer mids_level
        string physical_specimen_id
        string organisation_id
        string specimen_name
        string basis_of_record
    }

    Identification {
        string id
        string type
        string identification_id
        boolean is_verified_identification
        string date_identified
    }

    TaxonIdentification {
        string id
        string type
        string taxon_id
        string scientific_name
        string kingdom
        string family
        string genus
        string taxon_rank
    }

    Event {
        string id
        string type
        string event_type
        string event_date
        string habitat
        string sampling_protocol
    }

    Location {
        string id
        string type
        string country
        string state_province
        string locality
    }

    Georeference {
        string id
        string type
        float decimal_latitude
        float decimal_longitude
        string geodetic_datum
        float coordinate_uncertainty_in_meters
    }

    Agent {
        string id
        string type
        string agent_identifier
        string name
        string email
    }

    Assertion {
        string id
        string type
        string measurement_type
        string measurement_value
        string measurement_unit
    }

    Citation {
        string id
        string type
        string title
        string bibliographic_citation
    }

    DigitalSpecimen ||--o{ Identification : identifications
    DigitalSpecimen ||--o{ Event : events
    DigitalSpecimen ||--o{ Agent : agents
    DigitalSpecimen ||--o{ Assertion : assertions
    DigitalSpecimen ||--o{ Citation : citations
    Identification ||--o{ TaxonIdentification : taxon_identifications
    Identification ||--o{ Agent : agents
    Event ||--o| Location : location
    Location ||--o| Georeference : georeference

References

Resource	URL
DiSSCo Infrastructure	https://www.dissco.eu/
DiSSCo Schemas	https://schemas.dissco.tech/
Digital Specimen Schema	https://schemas.dissco.tech/schemas/fdo-type/digital-specimen/latest/
MIDS Specification	https://www.tdwg.org/community/cd/mids/
ROR (Research Organization Registry)	https://ror.org/

Usage

from metaseed import dissco

ds = dissco()

# Create DigitalSpecimen
specimen = ds.DigitalSpecimen(
    id="https://doi.org/10.22/specimen-001",
    type="ods:DigitalSpecimen",
    identifier="https://doi.org/10.22/specimen-001",
    version=1,
    created="2024-06-15T10:00:00Z",
    modified="2024-06-15T10:00:00Z",
    fdo_type="https://doi.org/10.22/fdo-type",
    mids_level=2,
    normalised_physical_specimen_id="NHMD-123456",
    physical_specimen_id="NHMD-123456",
    physical_specimen_id_type="Local",
    source_system_id="https://hdl.handle.net/source-system",
    organisation_id="https://ror.org/00example"
)

# Create Identification
identification = ds.Identification(
    type="ods:Identification",
    is_verified_identification=True,
    date_identified="2024-06-15"
)

# Create TaxonIdentification
taxon = ds.TaxonIdentification(
    type="ods:TaxonIdentification",
    scientific_name="Puma concolor (Linnaeus, 1771)",
    kingdom="Animalia",
    family="Felidae",
    genus="Puma",
    taxon_rank="species"
)