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Open Digital Specimen List of Terms

Source System List of Terms

Title : Source System List of Terms

Date version issued : 2024-10-15

Date created : 2024-10-15

This version : 0.4.0

Latest version : 0.4.0

Abstract : The Source System object provides information about the data providing system. Most important is the endpoint of the system through which we can retrieve the data and the data standard that is being used. At the moment the software supports the data standards: Darwin Core Archive and BioCASe endpoints. The Source System object points to the Mapping object which it uses to map the data correctly.

Main contributors : Sam Leeflang, Soulaine Theocharides, Tom Dijkema

Creator : Distributed Infrastructure for Scientific Collections (DiSSCo)

Bibliographic citation : Distributed Infrastructure for Scientific Collections. 2024. Source System List of Terms.

1 Introduction

1.1 Status of the content of this document

The openDS data specification is in active development. This document is work in progres and might change until version 1.0.0 is released. Its main function at the moment is to inform the community about the current state of the data model and to gather feedback. We hope to include the feedback from the community and reach a first major version of the data model by the end of 2024.

1.2 RFC 2119 key words

The key words “MUST”, “MUST NOT”, “REQUIRED”, “SHALL”, “SHALL NOT”, “SHOULD”, “SHOULD NOT”, “RECOMMENDED”, “MAY”, and “OPTIONAL” in this document are to be interpreted as described in BCP 14 RFC 2119 and RFC 8174 when, and only when, they appear in all capitals, as shown here.

2 Borrowed Vocabulary

When terms are borrowed from other vocabularies, openDS uses the IRIs, common abbreviations, and namespace prefixes in use in those vocabularies. The IRIs are normative, but abbreviations and namespace prefixes have no impact except as an aid to reading the documentation.

Table 1. Vocabularies from which terms have been borrowed (non-normative)

Vocabulary Abbreviation Namespaces and abbreviations
Latimer Core LtC lct: = http://rs.tdwg.org/ltc/terms/
Schema.org Schema schema: = https://schema.org/version/latest/schemaorg-current-https.rdf
Activity Streams AS as: = https://www.w3.org/ns/activitystreams#

3 Namespaces, Prefixes and Term Names

The namespace of terms borrowed from other vocabularies is that of the original. The namespace of de openDS terms is http://rs.dissco.eu/opends/terms/. In the table of terms, each term entry has a row with the term name. This term name is generally an “unqualified name” preceded by a widely accepted prefix designating an abbreviation for the namespace It is RECOMMENDED that implementers who need a namespace prefix for the openDS namespace use ods. In this web document, hovering over a term in the Index By Term Name list below will reveal a complete URL that can be used in other web documents to link to this document’s treatment of that term, even if it is from a borrowed vocabulary.

4 Term index

4.1 Index By Term Name

Classes
ods:Agent
ods:Identifier
ods:RelatedPID
ods:Role
ods:SourceSystem
ods:TombstoneMetadata

5 Vocabulary

Term Name schema:url
Qualified Term schema:url
Term IRI http://schema.org/url
Label URL
Definition URL to a website of the agent
Examples
  • https://dissco.eu
Datatype string
Belongs to Class ods:Agent
Required False
Repeatable False
RDF Type rdf:Property
Term Name Agent
Qualified Term ods:Agent
Term IRI http://rs.dissco.eu/opends/terms/Agent
Label Agent
Definition A generic agent class, containing information about the actor who performed an activity. This could be a person, an organization or a machine.
Required False
Repeatable True
RDF Type rdfs:Class
Term Name schema:identifier
Qualified Term schema:identifier
Term IRI http://schema.org/identifier
Label Identifier
Definition The primary unique identifier of the Agent object. All identifiers will also be added to the ods:hasIdentifiers array
Examples
  • http://www.wikidata.org/entity/Q66581882
  • https://orcid.org/0000-0002-1825-0097
  • https://hdl.handle.net/20.5000.1025/XXX-XXX-XXX
Datatype string
Belongs to Class ods:Agent
Required False
Repeatable False
RDF Type rdf:Property
Term Name schema:name
Qualified Term schema:name
Term IRI http://schema.org/name
Label Name
Definition Full name of the agent
Examples
  • John Smith
  • Sam Leeflang
Datatype string
Belongs to Class ods:Agent
Required False
Repeatable False
RDF Type rdf:Property
Term Name ods:hasRoles
Qualified Term ods:hasRoles
Term IRI http://rs.dissco.eu/opends/terms/hasRoles
Label Has Roles
Definition Contains all roles associated with the agent in the context of the Digital Object. Should always contain at least one role
Datatype array<ods:Role>
Belongs to Class ods:Agent
Required False
Repeatable False
RDF Type rdf:Property
Term Name schema:email
Qualified Term schema:email
Term IRI http://schema.org/email
Label Email
Definition Email of the agent
Examples
  • dissco@dissco.eu
Datatype string
Belongs to Class ods:Agent
Required False
Repeatable False
RDF Type rdf:Property
Term Name ods:hasIdentifiers
Qualified Term ods:hasIdentifiers
Term IRI http://rs.dissco.eu/opends/terms/hasIdentifiers
Label Has Identifiers
Definition Contains all identifiers associated with the agent
Datatype array<ods:Identifier>
Belongs to Class ods:Agent
Required False
Repeatable False
RDF Type rdf:Property
Term Name ods:gupriLevel
Qualified Term ods:gupriLevel
Term IRI http://rs.dissco.eu/opends/terms/gupriLevel
Label GUPRI Level
Definition Indicates whether the identifier is a persistent identifier
Controlled Vocabulary
  • LocallyUniqueStable
  • GloballyUniqueStable
  • GloballyUniqueStableResolvable
  • GloballyUniqueStablePersistentResolvable
  • GloballyUniqueStablePersistentResolvableFDOCompliant
Datatype string
Belongs to Class ods:Identifier
Required False
Repeatable False
RDF Type rdf:Property
Term Name ods:identifierStatus
Qualified Term ods:identifierStatus
Term IRI http://rs.dissco.eu/opends/terms/identifierStatus
Label Identifier Status
Definition Indicates the status of the identifier
Controlled Vocabulary
  • Preferred
  • Alternative
  • Superseded
Datatype string
Belongs to Class ods:Identifier
Required False
Repeatable False
RDF Type rdf:Property
Term Name dcterms:title
Qualified Term dcterms:title
Term IRI http://purl.org/dc/terms/title
Label Title
Definition A name for the identifier
Examples
  • abcd:UnitID
  • dwc:occurrenceID
  • ORCID
  • wikidata
  • ROR
  • cetaf stable identifier
Datatype string
Belongs to Class ods:Identifier
Required True
Repeatable False
RDF Type rdf:Property
Term Name dcterms:type
Qualified Term dcterms:type
Term IRI http://purl.org/dc/terms/type
Label Type
Definition The type of the value in the `dcterms:identifier` field
Examples
  • DOI
Controlled Vocabulary
  • ARK
  • arXiv
  • bibcode
  • DOI
  • EAN13
  • EISSN
  • Handle
  • IGSN
  • ISBN
  • ISSN
  • ISTC
  • LISSN
  • LSID
  • PMID
  • PURL
  • UPC
  • URL
  • URN
  • w3id
  • UUID
  • Other
  • Locally unique identifier
Datatype string
Belongs to Class ods:Identifier
Required False
Repeatable False
RDF Type rdf:Property
Term Name dcterms:identifier
Qualified Term dcterms:identifier
Term IRI http://purl.org/dc/terms/identifier
Label Identifier
Definition The value for the identifier
Examples
  • BMNH(E)1902475
  • RGM.800315
  • https://orcid.org/0000-0002-5669-2769
  • https://www.wikidata.org/wiki/Q66581882
  • https://ror.org/00bv4cx53
Datatype string
Belongs to Class ods:Identifier
Required False
Repeatable False
RDF Type rdf:Property
Term Name dcterms:format
Qualified Term dcterms:format
Term IRI http://purl.org/dc/terms/format
Label Format
Definition All possible mime types of content that can be returned by identifier in case the identifier is resolvable. Plain UUIDs for example do not have a dc:format return type, as they are not resolvable on their own. For a list of MIME types see the list maintained by IANA: http://www.iana.org/assignments/media-types/index.html, in particular the text http://www.iana.org/assignments/media-types/text/ and application http://www.iana.org/assignments/media-types/application/ types. Frequently used values are text/html, text/xml, application/rdf+xml, application/json
Examples
  • ['application/json', 'text/html']
  • ['application/rdf+xml', 'application/ld+json']
Datatype array<string>
Belongs to Class ods:Identifier
Required False
Repeatable False
RDF Type rdf:Property
Term Name dcterms:subject
Qualified Term dcterms:subject
Term IRI http://purl.org/dc/terms/subject
Label Subject
Definition Additional keywords that the publisher may prefer to be attached to the identifier
Examples
  • ['erecolnat', 'As available on label']
  • ['Registratie nummer', 'RMNH identifier']
Datatype array<string>
Belongs to Class ods:Identifier
Required False
Repeatable False
RDF Type rdf:Property
Term Name ods:isPartOfLabel
Qualified Term ods:isPartOfLabel
Term IRI http://rs.dissco.eu/opends/terms/isPartOfLabel
Label Is Part Of Label
Definition Indicates whether the identifier is part of the physical label
Datatype boolean
Belongs to Class ods:Identifier
Required False
Repeatable False
RDF Type rdf:Property
Term Name Identifier
Qualified Term ods:Identifier
Term IRI http://rs.dissco.eu/opends/terms/Identifier
Label Identifier
Definition A generic Identifier class which can be attached to multiple classes. It captures information about any identifier of the class.
Required False
Repeatable True
RDF Type rdfs:Class
Term Name ods:relationshipType
Qualified Term ods:relationshipType
Term IRI http://rs.dissco.eu/opends/terms/relationshipType
Label Relationship Type
Definition The type of relationship between the tombstoned object and the related object
Examples
  • RelatedTo
  • IsDuplicateOf
  • IsReplacedWith
Datatype string
Belongs to Class ods:RelatedPID
Required False
Repeatable False
RDF Type rdf:Property
Term Name schema:identifier
Qualified Term schema:identifier
Term IRI http://schema.org/identifier
Label Identifier
Definition The PID of the related object, used in cases of `ods:DataMapping`, `ods:SourceSystem` and `ods:MachineAnnotationService`
Examples
  • https://hdl.handle.net/20.5000.1025/XXX-XXX-XXX
Datatype string
Belongs to Class ods:RelatedPID
Required False
Repeatable False
RDF Type rdf:Property
Term Name RelatedPID
Qualified Term ods:RelatedPID
Term IRI http://rs.dissco.eu/opends/terms/RelatedPID
Label Related PID
Definition Indicates to which other Digital Object the tombstoned record is related to. This can be used when a digital object has been split or merged into other Digital Objects.
Required False
Repeatable True
RDF Type rdfs:Class
Term Name dcterms:identifier
Qualified Term dcterms:identifier
Term IRI http://purl.org/dc/terms/identifier
Label Identifier
Definition The PID of the related object, used in cases of `ods:Annotation`, `ods:DigitalMedia` and `ods:DigitalSpecimen`
Examples
  • https://doi.org/10.22/XXX-XXX-XXX
Datatype string
Belongs to Class ods:RelatedPID
Required True
Repeatable False
RDF Type rdf:Property
Term Name schema:endDate
Qualified Term schema:endDate
Term IRI http://schema.org/endDate
Label End Date
Definition Date the agent ended the role
Examples
  • 2023-09-02T12:31:34.806Z
Datatype string
Belongs to Class ods:Role
Required False
Repeatable False
RDF Type rdf:Property
Term Name Role
Qualified Term ods:Role
Term IRI http://rs.dissco.eu/opends/terms/Role
Label Role
Definition A role is a named entity that can be assigned to an agent. It is used to describe the function of an agent in a specific context.
Required False
Repeatable True
RDF Type rdfs:Class
Term Name schema:roleName
Qualified Term schema:roleName
Term IRI http://schema.org/roleName
Label Role Name
Definition The category that best matches the nature of a role of an Agent
Examples
  • collector
  • preparer
  • identifier
  • recorder
Datatype string
Belongs to Class ods:Role
Required False
Repeatable False
RDF Type rdf:Property
Term Name schema:startDate
Qualified Term schema:startDate
Term IRI http://schema.org/startDate
Label Start Date
Definition Date the agent began the role
Examples
  • 2023-10-02T12:31:34.806Z
Datatype string
Belongs to Class ods:Role
Required False
Repeatable False
RDF Type rdf:Property
Term Name schema:position
Qualified Term schema:position
Term IRI http://schema.org/position
Label Position
Definition Can be used to indicate the order of importance when there are multiple agents with the same role. Lower order means higher importance.
Examples
  • 1
  • 2
  • 3
Datatype integer
Belongs to Class ods:Role
Required False
Repeatable False
RDF Type rdf:Property
Term Name schema:identifier
Qualified Term schema:identifier
Term IRI http://schema.org/identifier
Label Identifier
Definition The unique identifier (handle) of the Source System object
Examples
  • https://hdl.handle.net/20.5000.1025/XXX-XXX-XXX
Datatype string
Belongs to Class ods:SourceSystem
Required True
Repeatable False
RDF Type rdf:Property
Term Name ods:fdoType
Qualified Term ods:fdoType
Term IRI http://rs.dissco.eu/opends/terms/fdoType
Label Fdo Type
Definition The DOI to the FDO type of the object
Examples
  • https://doi.org/10.15468/1a2b3c
Datatype string
Belongs to Class ods:SourceSystem
Required True
Repeatable False
RDF Type rdf:Property
Term Name ods:status
Qualified Term ods:status
Term IRI http://rs.dissco.eu/opends/terms/status
Label Status
Definition The status of the Digital Object. A digital object can be in Draft, when it is not published yet. Active when it is published and the object is active and Tombstone which means the object has been archived.
Controlled Vocabulary
  • Draft
  • Active
  • Tombstone
Datatype string
Belongs to Class ods:SourceSystem
Required False
Repeatable False
RDF Type rdf:Property
Term Name schema:version
Qualified Term schema:version
Term IRI http://schema.org/version
Label Version
Definition The version of the object, each change generates a new version. The version starts at 1 and each change will increment the version number with 1
Examples
  • 1
  • 2
  • 3
Datatype integer
Belongs to Class ods:SourceSystem
Required True
Repeatable False
RDF Type rdf:Property
Term Name schema:name
Qualified Term schema:name
Term IRI http://schema.org/name
Label Name
Definition Name of the Source System as provided by the user
Examples
  • Herbarium of University of Coimbra (COI)
  • Naturalis Biodiversity Center (NL) - Vermes
Datatype string
Belongs to Class ods:SourceSystem
Required False
Repeatable False
RDF Type rdf:Property
Term Name schema:description
Qualified Term schema:description
Term IRI http://schema.org/description
Label Description
Definition Description of the Source System as provided by the user
Examples
  • The herbarium collection of the University of Coimbra is one of the oldest in Portugal, with specimens dating back to the 18th century.
Datatype string
Belongs to Class ods:SourceSystem
Required False
Repeatable False
RDF Type rdf:Property
Term Name schema:dateCreated
Qualified Term schema:dateCreated
Term IRI http://schema.org/dateCreated
Label Date Created
Definition Timestamp of creation. Internally generated, https://schema.org/dateCreated
Examples
  • 2021-06-01T12:00:00.323Z
Datatype string
Belongs to Class ods:SourceSystem
Required True
Repeatable False
RDF Type rdf:Property
Term Name schema:dateModified
Qualified Term schema:dateModified
Term IRI http://schema.org/dateModified
Label Date Modified
Definition Timestamp of last modification. Internally generated, follows the ISO Date Time Format yyyy-MM-dd'T'HH:mm:ss.SSSXXX
Examples
  • 2021-06-06T13:22:00.445Z
Datatype string
Belongs to Class ods:SourceSystem
Required True
Repeatable False
RDF Type rdf:Property
Term Name schema:creator
Qualified Term schema:creator
Term IRI http://schema.org/creator
Label Creator
Definition Contains an ods:Agent object
Datatype object
Belongs to Class ods:SourceSystem
Required True
Repeatable False
RDF Type rdf:Property
Term Name SourceSystem
Qualified Term ods:SourceSystem
Term IRI http://rs.dissco.eu/opends/terms/SourceSystem
Label Source System
Definition The Source System describes the system from which the data is ingested. It contains information about the system, the endpoint and the data mapping.
Required True
Repeatable True
RDF Type rdfs:Class
Term Name ltc:collectionManagementSystem
Qualified Term ltc:collectionManagementSystem
Term IRI http://rs.tdwg.org/ltc/terms/collectionManagementSystem
Label Collection Management System
Definition The collection management system that the source system is using
Examples
  • Specify 7
Datatype string
Belongs to Class ods:SourceSystem
Required False
Repeatable False
RDF Type rdf:Property
Term Name ods:translatorType
Qualified Term ods:translatorType
Term IRI http://rs.dissco.eu/opends/terms/translatorType
Label Translator Type
Definition The serialisation of the data the endpoint provides indicating what type of Translator is required
Controlled Vocabulary
  • dwca
  • biocase
Datatype string
Belongs to Class ods:SourceSystem
Required True
Repeatable False
RDF Type rdf:Property
Term Name ods:maximumRecords
Qualified Term ods:maximumRecords
Term IRI http://rs.dissco.eu/opends/terms/maximumRecords
Label Maximum Records
Definition An optional parameter to limit the number of records to be ingested from this sourceSystem, it will pick the first X number of records it encounters. If left empty or absent it will process all records.
Datatype integer
Belongs to Class ods:SourceSystem
Required False
Repeatable False
RDF Type rdf:Property
Term Name ods:dataMappingID
Qualified Term ods:dataMappingID
Term IRI http://rs.dissco.eu/opends/terms/dataMappingID
Label Data Mapping ID
Definition The Handle of the Mapping Object needed for this Source System
Examples
  • https://hdl.handle.net/20.5000.1025/XXX-XXX-XXX
Datatype string
Belongs to Class ods:SourceSystem
Required True
Repeatable False
RDF Type rdf:Property
Term Name ods:hasTombstoneMetadata
Qualified Term ods:hasTombstoneMetadata
Term IRI http://rs.dissco.eu/opends/terms/hasTombstoneMetadata
Label Has Tombstone Metadata
Definition Object containing the tombstone metadata of the object. Only present when ods:status is ods:Tombstone
Datatype object
Belongs to Class ods:SourceSystem
Required False
Repeatable False
RDF Type rdf:Property
Term Name schema:url
Qualified Term schema:url
Term IRI http://schema.org/url
Label URL
Definition Endpoint from which data may be retrieved
Examples
  • http://ipt.gbif.pt/ipt/archive.do?r=coi
Datatype string
Belongs to Class ods:SourceSystem
Required True
Repeatable False
RDF Type rdf:Property
Term Name ods:hasAgents
Qualified Term ods:hasAgents
Term IRI http://rs.dissco.eu/opends/terms/hasAgents
Label Has Agents
Definition The agent(s) who tombstoned the Digital Object, contains an ods:Agent object
Datatype object
Belongs to Class ods:TombstoneMetadata
Required True
Repeatable False
RDF Type rdf:Property
Term Name TombstoneMetadata
Qualified Term ods:TombstoneMetadata
Term IRI http://rs.dissco.eu/opends/terms/TombstoneMetadata
Label Tombstone Metadata
Definition The tombstone metadata about the tombstoned digital object, including the what, who and when of the tombstoning.
Required False
Repeatable True
RDF Type rdfs:Class
Term Name ods:tombstoneDate
Qualified Term ods:tombstoneDate
Term IRI http://rs.dissco.eu/opends/terms/tombstoneDate
Label Tombstone Date
Definition Timestamp the Digital Object was tombstoned and no longer active. Following the ISO Date Time Format yyyy-MM-dd'T'HH:mm:ss.SSSXXX
Examples
  • 2021-06-01T12:00:000Z
Datatype string
Belongs to Class ods:TombstoneMetadata
Required True
Repeatable False
RDF Type rdf:Property
Term Name ods:tombstoneText
Qualified Term ods:tombstoneText
Term IRI http://rs.dissco.eu/opends/terms/tombstoneText
Label Tombstone Text
Definition A reason why the Digital Object was tombstoned
Examples
  • This is a duplicate of XXX
  • This object was made by mistake
Datatype string
Belongs to Class ods:TombstoneMetadata
Required True
Repeatable False
RDF Type rdf:Property
Term Name ods:hasRelatedPIDs
Qualified Term ods:hasRelatedPIDs
Term IRI http://rs.dissco.eu/opends/terms/hasRelatedPIDs
Label Has Related Pi Ds
Definition The PIDs of the object the tombstoned object is related to
Datatype array<ods:RelatedPID>
Belongs to Class ods:TombstoneMetadata
Required False
Repeatable False
RDF Type rdf:Property