Digital Specimen update to 0.2.0 #92
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| # Release Notes | ||
|
|
||
| New version 0.0.2 for some of the files to include new terms. | ||
|
|
||
| ## Verbatim Terms | ||
| Verbatim terms added such as `dwc:verbatimLocality` and `dwc:verbatimEventDate`. | ||
| The verbatim terms will be filled with the verbatim fields but not used for any further processing. | ||
| They are mainly used to keep the original value on the label. | ||
| The non-verbatim fields will be used for further processing. | ||
| For the non-verbatim fields we will first check the non-verbatim field, if this is not available we will take the verbatim field. | ||
| For example, to fill the `dwc:locality` field we will first check the `dwc:locality` field, if this is empty we will take the `dwc:verbatimLocality` field. | ||
|
|
||
| ## ID fields | ||
| MIDS 3 requires several ID fields to be present. | ||
| These were not all included in the 0.1.0 version. | ||
|
|
||
| ## Updated class names | ||
| Updated class names to reuse Darwin Core classes as much as possible. | ||
| Where it is not possible to reuse Darwin Core we prefixed them with `???:`. | ||
| Made them singular and camelCase. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,336 @@ | ||
| { | ||
| "$id": "https://schemas.dissco.tech/schemas/digitalobjects/0.2.0/digital-specimens/digital-specimen.json", | ||
| "$schema": "https://json-schema.org/draft/2020-12/schema", | ||
| "$comment":"DigitalObject Version 0.2.0", | ||
| "type": "object", | ||
| "properties": { | ||
| "ods:id": { | ||
| "type": "string", | ||
| "description": "The unique digital identifier of the object", | ||
| "pattern": "https:\/\/doi.org\/10.22\/(.){3}-(.){3}-(.){3}", | ||
| "examples": [ | ||
| "https://doi.org/10.22/XXX-XXX-XXX" | ||
| ] | ||
| }, | ||
| "ods:version": { | ||
| "type": "integer", | ||
| "description": "The version of the object, each change generates a new version", | ||
| "minimum": 1, | ||
| "examples": [ | ||
| 1 | ||
| ] | ||
| }, | ||
| "ods:created": { | ||
| "type": "string", | ||
| "description": "The timestamp that the object version was created in DiSSCo", | ||
| "format": "date-time", | ||
| "examples": [ | ||
| "2023-10-02T12:31:34.806Z" | ||
| ] | ||
| }, | ||
| "ods:type": { | ||
| "type": "string", | ||
| "description": "The FDO type of the object", | ||
| "$comment": "Unclear what value goes here" | ||
| }, | ||
| "ods:midsLevel": { | ||
| "type": "integer", | ||
| "description": "The MIDS level of the object, see https://www.tdwg.org/community/cd/mids/", | ||
| "minimum": 0, | ||
| "maximum": 3 | ||
| }, | ||
| "ods:normalisedPhysicalSpecimenId": { | ||
| "type": "string", | ||
| "description": "The physical specimen identifier of the object. When locally unique this is a combination between source-system-id and the local identifier" | ||
| }, | ||
| "ods:physicalSpecimenId": { | ||
| "type": "string", | ||
| "description": "The physical specimen identifier of the object. Taken over as-is" | ||
| }, | ||
| "ods:physicalSpecimenIdType": { | ||
| "type": "string", | ||
| "description": "To indicate if the physical identifier is globally unique or locally unique", | ||
| "enum": [ | ||
| "Resolvable", | ||
| "Global", | ||
| "Local" | ||
| ], | ||
| "$comment": "Do we need to further distinguish the identifier, for example add 'RESOLVABLE'" | ||
| }, | ||
| "ods:topicOrigin": { | ||
| "type": "string", | ||
| "description": "The topic origin of the specimen", | ||
| "enum": [ | ||
| "Natural", | ||
| "Human-made", | ||
| "Mixed origin", | ||
| "Unclassified" | ||
| ], | ||
| "example": [ | ||
| "Natural" | ||
| ] | ||
| }, | ||
| "ods:topicDomain": { | ||
| "type": "string", | ||
| "description": "The topic domain of the specimen", | ||
| "enum": [ | ||
| "Life", | ||
| "Environment", | ||
| "Earth System", | ||
| "Extraterrestrial", | ||
| "Cultural Artefacts", | ||
| "Archive Material", | ||
| "Unclassified" | ||
| ], | ||
| "example": [ | ||
| "Life" | ||
| ] | ||
| }, | ||
| "ods:topicDiscipline": { | ||
| "type": "string", | ||
| "description": "The topic discipline of the specimen", | ||
| "enum": [ | ||
| "Anthropology", | ||
| "Botany", | ||
| "Astrogeology", | ||
| "Geology", | ||
| "Microbiology", | ||
| "Palaeontology", | ||
| "Zoology", | ||
| "Ecology", | ||
| "Other Biodiversity", | ||
| "Other Geodiversity", | ||
| "Unclassified" | ||
| ], | ||
| "example": [ | ||
| "Botany" | ||
| ] | ||
| }, | ||
| "ods:markedAsType": { | ||
| "type": "boolean", | ||
| "description": "The specimen is marked as a type specimen" | ||
| }, | ||
| "ods:hasMedia": { | ||
| "type": "boolean", | ||
| "description": "Indicates if there are any media objects attached to this specimen" | ||
| }, | ||
| "ods:specimenName": { | ||
| "type": "string", | ||
| "description": "The accepted specimen name of the digital specimen", | ||
| "example": [ | ||
| "Roptrocerus typographi (Györfi, 1952)" | ||
| ] | ||
| }, | ||
| "ods:sourceSystem": { | ||
| "type": "string", | ||
| "description": "The handle to the source system object which retrieved the data from the CMS", | ||
| "pattern": "https:\/\/hdl.handle.net\/20.5000.1025\/(.){3}-(.){3}-(.){3}" | ||
| }, | ||
| "ods:livingOrPreserved": { | ||
| "type": "string", | ||
| "description": "Whether the specimen is living or preserved", | ||
| "enum": [ | ||
| "Living", | ||
| "Preserved" | ||
| ] | ||
| }, | ||
| "dcterms:license": { | ||
| "type": "string", | ||
| "description": "License for the metadata of the physical specimen", | ||
| "$comment": "Determine available licenses" | ||
| }, | ||
| "dcterms:modified": { | ||
| "type": "string", | ||
| "description": "Modification date for specimen information" | ||
| }, | ||
| "dwc:basisOfRecord": { | ||
| "type": "string", | ||
| "description": "The basis for the record", | ||
| "$comment": "Switch to enumeration as this is a limited list" | ||
| }, | ||
| "dwc:preparations": { | ||
| "type": "string", | ||
| "description": "https://rs.tdwg.org/dwc/terms/preparations", | ||
| "example": [ | ||
| "fossil" | ||
| ] | ||
| }, | ||
| "dwc:disposition": { | ||
| "type": "string", | ||
| "description": "https://rs.tdwg.org/dwc/terms/disposition", | ||
| "examples": [ | ||
| "in collection" | ||
| ] | ||
| }, | ||
| "dwc:institutionCode": { | ||
| "type": "string", | ||
| "description": "https://rs.tdwg.org/dwc/terms/institutionCode", | ||
| "examples": [ | ||
| "MNF" | ||
| ] | ||
| }, | ||
| "dwc:institutionId": { | ||
| "type": "string", | ||
| "description": "ROR or Wikidata identifier, based on https://rs.tdwg.org/dwc/terms/institutionID", | ||
| "examples": [ | ||
| "https://ror.org/015hz7p22" | ||
| ], | ||
| "$comment": "Add format for ROR or Wikidata ID" | ||
| }, | ||
| "dwc:institutionName": { | ||
| "type": "string", | ||
| "description": "Full museum name according to ROR or Wikidata", | ||
| "examples": [ | ||
| "National Museum of Natural History" | ||
| ], | ||
| "$comment": "Not part of DWC or the GBIF UM" | ||
| }, | ||
| "dwc:collectionCode": { | ||
| "type": "string", | ||
| "description": "https://rs.tdwg.org/dwc/terms/collectionCode", | ||
| "examples": [ | ||
| "EBIRD" | ||
| ], | ||
| "$comment": "Cetaf collection code?" | ||
| }, | ||
| "dwc:collectionId": { | ||
| "type": "string", | ||
| "description": "https://rs.tdwg.org/dwc/terms/collectionID", | ||
| "examples": [ | ||
| "https://www.gbif.org/grscicoll/collection/fbd3ed74-5a21-4e01-b86a-33d36f032d9c" | ||
| ], | ||
| "$comment": "Are we going to use GRSciColl or Cetaf collection identifiers?" | ||
| }, | ||
| "dwc:informationWithheld": { | ||
| "type": "string", | ||
| "description": "https://rs.tdwg.org/dwc/terms/informationWithheld", | ||
| "examples": [ | ||
| "location information not given for endangered species" | ||
| ], | ||
| "$comment": "Feels like this field should be true or false and another field should contain the explanation" | ||
| }, | ||
| "dwc:dataGeneralizations": { | ||
| "type": "string", | ||
| "description": "https://rs.tdwg.org/dwc/terms/dataGeneralizations", | ||
| "examples": [ | ||
| "Coordinates generalized from original GPS coordinates to the nearest half degree grid cell." | ||
| ] | ||
| }, | ||
| "dwc:ownerInstitutionId": { | ||
| "type": "string", | ||
| "description": "ROR or Wikidata identifier for the owning institution", | ||
| "$comment": "DWC only has ownerInstitutionCode, however code is not an (resolvable identifier)", | ||
| "examples": [ | ||
| "https://ror.org/03wkt5x30" | ||
| ] | ||
| }, | ||
| "dwc:recordedBy": { | ||
| "type": "string", | ||
| "description": "https://rs.tdwg.org/dwc/terms/recordedBy", | ||
| "examples": [ | ||
| "José E. Crespo" | ||
| ] | ||
| }, | ||
| "dwc:recordedById": { | ||
| "type": "string", | ||
| "description": "https://rs.tdwg.org/dwc/terms/recordedByID", | ||
| "examples": [ | ||
| "https://orcid.org/0000-0002-1825-0097" | ||
| ] | ||
| }, | ||
| "dwc:datasetName": { | ||
| "type": "string", | ||
| "description": "https://rs.tdwg.org/dwc/terms/datasetName", | ||
| "examples": [ | ||
| "Hummingbirds" | ||
| ] | ||
| }, | ||
| "dcterms:accessRights": { | ||
| "type": "string", | ||
| "description": "https://purl.org/dc/terms/accessRights", | ||
| "examples": [ | ||
| "not-for-profit use only" | ||
| ] | ||
| }, | ||
| "dcterms:rightsHolder": { | ||
| "type": "string", | ||
| "description": "https://purl.org/dc/terms/rightsHolder", | ||
| "examples": [ | ||
| "Museu de História Natural e da Ciência da Universidade do Porto" | ||
| ] | ||
| }, | ||
| "dwc:verbatimLabel": { | ||
| "type": "string", | ||
| "description": "https://rs.tdwg.org/dwc/terms/verbatimLabel", | ||
| "examples": [ | ||
| "ILL: Union Co. Wolf Lake by Powder Plant Bridge. 1 March 1975 Coll. S. Ketzler, S. Herbert\n\nMonotoma longicollis 4 ♂ Det TC McElrath 2018\n\nINHS Insect Collection 456782" | ||
| ] | ||
| }, | ||
| "dwc:MaterialEntity": { | ||
| "type": "array", | ||
| "items": { | ||
| "$ref": "https://schemas.dissco.tech/schemas/digitalobjects/0.2.0/digital-specimens/material-entity.json" | ||
| } | ||
| }, | ||
| "dwc:Identification": { | ||
| "type": "array", | ||
| "items": { | ||
| "$ref": "https://schemas.dissco.tech/schemas/digitalobjects/0.2.0/digital-specimens/identifications.json" | ||
| } | ||
| }, | ||
| "???:Assertion": { | ||
| "type": "array", | ||
| "items": { | ||
| "$ref": "https://schemas.dissco.tech/schemas/digitalobjects/0.1.0/shared-models/assertions.json" | ||
| } | ||
| }, | ||
| "dwc:Occurrence": { | ||
| "type": "array", | ||
| "items": { | ||
| "$ref": "https://schemas.dissco.tech/schemas/digitalobjects/0.2.0/digital-specimens/occurrences.json" | ||
| } | ||
| }, | ||
| "???:EntityRelationship": { | ||
|
There was a problem hiding this comment. should we mark this gbif:EntityRelationship to indicate that they are from the new data model? |
||
| "type": "array", | ||
| "items": { | ||
| "$ref": "https://schemas.dissco.tech/schemas/digitalobjects/0.1.0/shared-models/entity-relationships.json" | ||
| } | ||
| }, | ||
| "???:Citation": { | ||
| "type": "array", | ||
| "items": { | ||
| "$ref": "https://schemas.dissco.tech/schemas/digitalobjects/0.1.0/shared-models/citations.json" | ||
| } | ||
| }, | ||
| "???:Identifier": { | ||
| "type": "array", | ||
| "items": { | ||
| "$ref": "https://schemas.dissco.tech/schemas/digitalobjects/0.1.0/shared-models/identifiers.json" | ||
| } | ||
| }, | ||
| "???:ChronometricAge": { | ||
| "type": "array", | ||
| "items": { | ||
| "$ref": "https://schemas.dissco.tech/schemas/digitalobjects/0.1.0/digital-specimens/chronometric-age.json" | ||
| } | ||
| }, | ||
| "???:Agent": { | ||
| "type": "array", | ||
| "items": { | ||
| "$ref": "https://schemas.dissco.tech/schemas/digitalobjects/0.1.0/shared-models/agent.json" | ||
| } | ||
| } | ||
| }, | ||
| "required": [ | ||
| "ods:id", | ||
| "ods:version", | ||
| "ods:type", | ||
| "ods:created", | ||
| "ods:midsLevel", | ||
| "ods:physicalSpecimenId", | ||
| "ods:physicalSpecimenIdType", | ||
| "ods:sourceSystem", | ||
| "dcterms:license", | ||
| "dwc:institutionId" | ||
| ] | ||
| } | ||
Oops, something went wrong.
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
yes, but the example shows as text desc. so let's use it with text for now.