Digital Specimen Core Resources
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Digital Specimen Resources
This page contains an assortment of resources to help explain the structure and relationship of the Digital Media object.
Latimer Core Resources
This page contains an assortment of resources to help facilitate activities associated with the Latimer Core standard.
SSSOM
SKOS Mappings metadata elements based on Simple Standard for Sharing Ontological Mappings (SSSOM)
DiSSCo has developed three SSSOM mappings to other data standards: DwC-A, ABCD(EFG), DwC-DP. For each of these there is a tsv available for the 0.4.0 version of the Digital Specimen and Digital Media object. The basis for this mapping is the logic developed in the DiSSCo Translator.
- Darwin Core Archive: https://schemas.dissco.tech/schemas/data-mapping/0.4.0/sssom_dwca.tsv
- Access to Biological Collection Data (ABCD) + Extension for Geosciences (EFG) : https://schemas.dissco.tech/schemas/data-mapping/0.4.0/sssom_abcdefg.tsv
- Darwin Core Data Package: https://schemas.dissco.tech/schemas/data-mapping/0.4.0/sssom_dwc_dp.tsv
More information on the SSSOM standard can be found here:
- Specification: https://mapping-commons.github.io/sssom/
- Repository: https://github.com/mapping-commons/sssom
- Citation: Nicolas Matentzoglu, James P Balhoff, Susan M Bello, Chris Bizon, Matthew Brush, Tiffany J Callahan, Christopher G Chute, William D Duncan, Chris T Evelo, Davera Gabriel, John Graybeal, Alasdair Gray, Benjamin M Gyori, Melissa Haendel, Henriette Harmse, Nomi L Harris, Ian Harrow, Harshad B Hegde, Amelia L Hoyt, Charles T Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Koehler, Thomas Liener, Qinqin Long, James Malone, James A McLaughlin, Julie A McMurry, Sierra Moxon, Monica C Munoz-Torres, David Osumi-Sutherland, James A Overton, Bjoern Peters, Tim Putman, Núria Queralt-Rosinach, Kent Shefchek, Harold Solbrig, Anne Thessen, Tania Tudorache, Nicole Vasilevsky, Alex H Wagner, Christopher J Mungall, A Simple Standard for Sharing Ontological Mappings (SSSOM), Database, Volume 2022, 2022, baac035, https://doi.org/10.1093/database/baac035
Diagrams
Class Diagrams
classDiagram
class DigitalSpecimen {
dcterms:identifier : string
ods:version : integer
ods:status : string
dcterms:modified : string
dcterms:created : string
ods:fdoType : string
ods:midsLevel : integer
ods:normalisedPhysicalSpecimenID : string
ods:physicalSpecimenID : string
ods:physicalSpecimenIDType : string
ods:isKnownToContainMedia : boolean
ods:sourceSystemID : string
ods:sourceSystemName : string
ods:livingOrPreserved : string
ods:metadataLanguages : array<string>
dcterms:license : string
dwc:basisOfRecord : string
ods:organisationCode : string
ods:organisationID : string
ods:organisationName : string
dwc:collectionCode : string
dwc:collectionID : string
ods:topicOrigin : string
ods:topicDomain : string
ods:topicDiscipline : string
ods:topicCategory : string
ods:specimenName : string
dwc:informationWithheld : string
dwc:preparations : string
dwc:disposition : string
ods:isMarkedAsType : boolean
dwc:dataGeneralizations : string
ods:ownerOrganisationCode : string
dwc:datasetName : string
dwc:datasetID : string
dcterms:accessRights : string
dcterms:rightsHolder : string
dwc:organismID : string
dwc:organismName : string
dwc:organismScope : string
dwc:organismRemarks : string
dwc:organismQuantity : string
dwc:organismQuantityType : string
dwc:verbatimLabel : string
dwc:dynamicProperties : string
ods:hasSpecimenParts : array<ods:SpecimenPart>
ods:hasAssertions : array<ods:Assertion>
ods:hasEntityRelationships : array<ods:EntityRelationship>
ods:hasIdentifications : array<ods:Identification>
ods:hasIdentifiers : array<ods:Identifier>
ods:hasCitations : array<ods:Citation>
ods:hasAgents : array<ods:Agent>
ods:hasEvents : array<ods:Event>
ods:hasChronometricAges : array<ods:ChronometricAge>
ods:hasTombstoneMetadata : object
}
class SpecimenPart {
dwc:materialEntityID : string
dwc:recordNumber : string
dwc:preparations : string
ods:isMarkedAsType : boolean
ods:topicOrigin : string
ods:topicDomain : string
ods:topicDiscipline : string
ods:topicCategory : string
ods:specimenName : string
dwc:organismID : string
dwc:organismName : string
dwc:organismScope : string
dwc:organismRemarks : string
dwc:organismQuantity : string
dwc:organismQuantityType : string
ods:hasIdentifications : array<ods:Identification>
ods:hasAssertions : array<ods:Assertion>
ods:hasIdentifiers : array<ods:Identifier>
ods:hasEvents : array<ods:Event>
ods:hasAgents : array<ods:Agent>
ods:hasChronometricAges : array<ods:ChronometricAge>
}
class Identification {
dwc:identificationID : string
ods:identificationType : string
dwc:verbatimIdentification : string
dwc:typeStatus : string
dwc:dateIdentified : string
ods:isVerifiedIdentification : boolean
dwc:identificationRemarks : string
dwc:identificationQualifier : string
ods:hasAgents : array<ods:Agent>
ods:hasCitations : array<ods:Citation>
ods:hasTaxonIdentifications : array<ods:TaxonIdentification>
}
class Event {
dwc:behavior : string
dwc:eventType : string
dwc:sex : string
dwc:lifeStage : string
dwc:reproductiveCondition : string
dwc:caste : string
dwc:vitality : string
dwc:establishmentMeans : string
dwc:pathway : string
dwc:degreeOfEstablishment : string
dwc:georeferenceVerificationStatus : string
dwc:fieldNumber : string
dwc:eventDate : string
dwc:eventTime : string
dwc:endDayOfYear : integer
dwc:startDayOfYear : integer
dwc:verbatimEventDate : string
dwc:year : integer
dwc:month : integer
dwc:day : integer
dwc:habitat : string
eco:protocolDescriptions : string
dwc:sampleSizeValue : number
dwc:sampleSizeUnit : string
dwc:samplingProtocol : string
dwc:samplingEffort : string
dwc:fieldNotes : string
dwc:eventRemarks : string
ods:hasAssertions : array<ods:Assertion>
ods:hasAgents : array<ods:Agent>
ods:hasLocation : object
}
class Location {
dwc:locationID : string
dwc:continent : string
dwc:waterBody : string
dwc:islandGroup : string
dwc:island : string
dwc:country : string
dwc:countryCode : string
dwc:stateProvince : string
dwc:county : string
dwc:municipality : string
dwc:locality : string
dwc:verbatimLocality : string
dwc:minimumElevationInMeters : number
dwc:higherGeographyID : string
dwc:higherGeography : string
dwc:maximumElevationInMeters : number
dwc:verbatimElevation : string
dwc:minimumDistanceAboveSurfaceInMeters : number
dwc:maximumDistanceAboveSurfaceInMeters : number
dwc:minimumDepthInMeters : number
dwc:maximumDepthInMeters : number
dwc:verbatimDepth : string
dwc:verticalDatum : string
dwc:locationAccordingTo : string
dwc:locationRemarks : string
ods:hasGeoreference : object
ods:hasGeologicalContext : object
}
class Agent {
schema:identifier : string
schema:name : string
ods:hasRoles : array<ods:Role>
schema:email : string
schema:url : string
ods:hasIdentifiers : array<ods:Identifier>
}
class Role {
schema:roleName : string
schema:startDate : string
schema:endDate : string
schema:position : integer
}
class Assertion {
dwc:measurementID : string
dwc:parentMeasurementID : string
dwc:measurementType : string
dwciri:measurementType : string
dwc:measurementDeterminedDate : string
dwc:measurementValue : string
dwciri:measurementValue : string
dwc:measurementAccuracy : string
dwc:measurementUnit : string
dwciri:measurementUnit : string
dwc:measurementMethod : string
dwciri:measurementMethod : string
dwc:measurementRemarks : string
ods:hasAgents : array<ods:Agent>
ods:hasCitations : array<ods:Citation>
}
class Citation {
dcterms:identifier : string
dcterms:type : string
dcterms:date : string
dcterms:title : string
ods:pageNumber : string
dcterms:description : string
dcterms:bibliographicCitation : string
ods:isPeerReviewed : boolean
ods:hasAgents : array<ods:Agent>
}
class EntityRelationship {
dwc:relationshipOfResource : string
dwc:relationshipOfResourceID : string
dwc:relatedResourceID : string
ods:relatedResourceURI : string
dwc:relationshipEstablishedDate : string
dwc:relationshipRemarks : string
ods:hasAgents : array<ods:Agent>
}
class Identifier {
dcterms:title : string
dcterms:type : string
dcterms:identifier : string
dcterms:format : array<string>
dcterms:subject : array<string>
ods:isPartOfLabel : boolean
ods:gupriLevel : string
ods:identifierStatus : string
}
class ChronometricAge {
chrono:chronometricAgeID : string
chrono:verbatimChronometricAge : string
chrono:uncalibratedChronometricAge : string
chrono:chronometricAgeConversionProtocol : string
chrono:earliestChronometricAge : integer
chrono:earliestChronometricAgeReferenceSystem : string
chrono:latestChronometricAge : integer
chrono:latestChronometricAgeReferenceSystem : string
chrono:chronometricAgeProtocol : string
chrono:chronometricAgeUncertaintyInYears : integer
chrono:chronometricAgeUncertaintyMethod : string
chrono:materialDated : string
chrono:materialDatedID : string
chrono:materialDatedRelationship : string
chrono:chronometricAgeDeterminedDate : string
chrono:chronometricAgeReferences : string
chrono:chronometricAgeRemarks : string
ods:hasAgents : array<ods:Agent>
}
class TombstoneMetadata {
ods:tombstoneDate : string
ods:tombstoneText : string
ods:hasAgents : array<ods:Agent>
ods:hasRelatedPIDs : array<ods:RelatedPID>
}
class RelatedPID {
dcterms:identifier : string
schema:identifier : string
ods:relationshipType : string
}
class TaxonIdentification {
dwc:taxonID : string
dwc:scientificName : string
dwc:scientificNameID : string
ods:scientificNameHTMLLabel : string
ods:genusHTMLLabel : string
dwc:scientificNameAuthorship : string
dwc:namePublishedInYear : string
dwc:taxonRank : string
dwc:verbatimTaxonRank : string
dwc:taxonRemarks : string
dwc:kingdom : string
dwc:phylum : string
dwc:class : string
dwc:order : string
dwc:family : string
dwc:subfamily : string
dwc:genus : string
dwc:specificEpithet : string
dwc:taxonomicStatus : string
dwc:nomenclaturalCode : string
dwc:vernacularName : string
dwc:subgenus : string
dwc:acceptedNameUsage : string
dwc:acceptedNameUsageID : string
dwc:cultivarEpithet : string
dwc:genericName : string
dwc:infragenericEpithet : string
dwc:infraspecificEpithet : string
dwc:nomenclaturalStatus : string
dwc:originalNameUsage : string
dwc:subtribe : string
dwc:superfamily : string
dwc:tribe : string
}
class GeologicalContext {
dwc:earliestEonOrLowestEonothem : string
dwc:latestEonOrHighestEonothem : string
dwc:earliestEraOrLowestErathem : string
dwc:latestEraOrHighestErathem : string
dwc:earliestPeriodOrLowestSystem : string
dwc:latestPeriodOrHighestSystem : string
dwc:earliestEpochOrLowestSeries : string
dwc:latestEpochOrHighestSeries : string
dwc:earliestAgeOrLowestStage : string
dwc:latestAgeOrHighestStage : string
dwc:lowestBiostratigraphicZone : string
dwc:highestBiostratigraphicZone : string
dwc:lithostratigraphicTerms : string
dwc:group : string
dwc:formation : string
dwc:member : string
dwc:bed : string
}
class Georeference {
dwc:verbatimCoordinates : string
dwc:decimalLatitude : number
dwc:verbatimLatitude : string
dwc:decimalLongitude : number
dwc:verbatimLongitude : string
dwc:verbatimCoordinateSystem : string
dwc:geodeticDatum : string
dwc:coordinateUncertaintyInMeters : number
dwc:coordinatePrecision : number
dwc:pointRadiusSpatialFit : number
dwc:footprintWKT : string
dwc:footprintSRS : string
dwc:verbatimSRS : string
dwc:footprintSpatialFit : integer
dwc:georeferencedDate : string
dwc:georeferenceProtocol : string
dwc:georeferenceSources : string
dwc:georeferenceRemarks : string
ods:hasAgents : array<ods:Agent>
}
DigitalSpecimen -- SpecimenPart
DigitalSpecimen -- Identification
DigitalSpecimen -- Event
DigitalSpecimen -- Citation
DigitalSpecimen -- Identifier
DigitalSpecimen -- Assertion
DigitalSpecimen -- Agent
DigitalSpecimen -- EntityRelationship
DigitalSpecimen -- ChronometricAge
DigitalSpecimen -- TombstoneMetadata
TombstoneMetadata -- Agent
TombstoneMetadata -- RelatedPID
Event -- Location
Event -- Assertion
Location -- Georeference
Location -- GeologicalContext
Agent -- Identifier
Agent -- Role
Identification -- Citation
Citation -- Agent
Identification -- Agent
Identification -- TaxonIdentification
Assertion -- Agent
Assertion -- Citation
Citation -- Agent
EntityRelationship -- Agent
Georeference -- Agent
Agent -- Identifier
SpecimenPart -- Identification
SpecimenPart -- Assertion
SpecimenPart -- Agent
SpecimenPart -- ChronometricAge
SpecimenPart -- Identifier
SpecimenPart -- Event
Entity-Relationship Diagrams
erDiagram
DigitalSpecimen ||--o{ SpecimenPart : Has
DigitalSpecimen ||--o{ Identification : Has
DigitalSpecimen ||--o{ Event : Has
DigitalSpecimen ||--o{ Citation : Has
DigitalSpecimen ||--|{ Identifier : Has
DigitalSpecimen ||--o{ Assertion : Has
DigitalSpecimen ||--o{ Agent : Has
DigitalSpecimen ||--o{ EntityRelationship : Has
DigitalSpecimen ||--o{ ChronometricAge : Has
DigitalSpecimen ||--o| TombstoneMetadata : Has
TombstoneMetadata ||--|{ Agent : Has
TombstoneMetadata ||--o{ RelatedPID : Has
Event ||--o| Location : Has
Event ||--o{ Assertion : Has
Location ||--o| Georeference : Has
Location ||--o| GeologicalContext : Has
Agent ||--o{ Identifier : Has
Agent ||--|{ Role : Has
Identification ||--o{ Citation : Has
Citation ||--o{ Agent : Has
Identification ||--o{ Agent : Has
Identification ||--o{ TaxonIdentification : Has
Assertion ||--o{ Agent : Has
Assertion ||--o{ Citation : Has
EntityRelationship ||--|{ Agent : Has
Georeference ||--o{ Agent : Has
SpecimenPart ||--o{ Identification : Has
SpecimenPart ||--o{ Assertion : Has
SpecimenPart ||--o{ Agent : Has
SpecimenPart ||--o{ ChronometricAge : Has
SpecimenPart ||--o{ Identifier : Has
SpecimenPart ||--o{ Event : Has
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