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Merge branch 'master' into rfc2119

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Steve Baskauf 2021-08-05 10:21:34 -05:00
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@ -12,7 +12,7 @@
8. Repeat this process for all namespaces that will be changed. I've been saving copies of the changes in [this directory](https://github.com/tdwg/rs.tdwg.org/tree/master/process/dwc-revisions) so that we can easily see what's been done in the past. Modify the [configuration file](https://github.com/tdwg/rs.tdwg.org/blob/master/process/config.json) so that it points to each CSV for each namespace. Look at the example to see what needs to be there.
9. Run the [processing script](https://github.com/tdwg/rs.tdwg.org/blob/master/process/process.py), which needs to be in the same directory as the configuration file.
10. There are some manual edits that need to be made if there are changes to either of the Dublin Core namespace terms. The versions don't get handled very automatically, so make the same changes to the [dcterms: version CSV](https://github.com/tdwg/rs.tdwg.org/blob/master/dcterms-for-dwc-versions/dcterms-for-dwc-versions.csv) or [dc: version CSV](https://github.com/tdwg/rs.tdwg.org/blob/master/dc-for-dwc-versions/dc-for-dwc-versions.csv) as were made to the main term CSVs.
11. The versions also need to be manually added for the new termlist version in the [termlist versions members CSV](https://github.com/tdwg/rs.tdwg.org/blob/master/term-lists-versions/term-lists-versions-members.csv). In the future, this may get automated.
11. The Dublin Core versions also need to be manually added for the new termlist version in the [termlist versions members CSV](https://github.com/tdwg/rs.tdwg.org/blob/master/term-lists-versions/term-lists-versions-members.csv). In the future, this may get automated.
12. As of 2020-08-20, updating rs.tdwg.org document metadata must be done manually. Steve Baskauf knows how to do it and will try to eventually write a script to automate the process. It's best to ask him to do the updating before merging the branch.
13. Push the branch to GitHub and create a pull request. It is best for someone to review the changes carefully before merging.
14. Once the branch has been merged the data are available via HTTP to the other scripts that use those data.
@ -65,4 +65,4 @@ It generates the file `term_versions.csv`, which is used as the input for the `b
The Python script `build-termlist.py` inputs the header information from `termlist-header.md`, then builds the list of terms and their metadata from data in the [rs.tdwg.org](http://github.com/tdwg/rs.tdwg.org) repository. The script also inputs `termlist-footer.md` and appends it to the end of the generated document, but currently it has no content. The constructed Markdown document is saved as `/docs/list/index.md`.
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@ -4,7 +4,7 @@ Title
: Darwin Core RDF guide
Date version issued
: 2016-04-25
: 2021-07-15
Date created
: 2015-03-27
@ -13,13 +13,13 @@ Part of TDWG Standard
: <http://www.tdwg.org/standards/450/>
This version
: <http://rs.tdwg.org/dwc/terms/guides/rdf/2015-06-02>
: <http://rs.tdwg.org/dwc/terms/guides/rdf/2021-07-15>
Latest version
: <http://rs.tdwg.org/dwc/terms/guides/rdf/>
Previous version
: <http://rs.tdwg.org/dwc/terms/guides/rdf/2015-03-27>
: <http://rs.tdwg.org/dwc/terms/guides/rdf/2016-04-25>
Abstract
: This guide is intended to facilitate the use of Darwin Core terms in the Resource Description Framework (RDF). It explains basic features of RDF and provides details of how to expose data in the form of RDF using Darwin Core terms and terms from other key vocabularies. It defines terms in the namespace `http://rs.tdwg.org/dwc/iri/` which are intended for use exclusively with non-literal objects.
@ -31,7 +31,7 @@ Creator
: Darwin Core and RDF/OWL Task Groups
Bibliographic citation
: Darwin Core and RDF/OWL Task Groups. 2015. Darwin Core RDF guide. Biodiversity Information Standards (TDWG). <http://rs.tdwg.org/dwc/terms/guides/rdf/>
: Darwin Core and RDF/OWL Task Groups. 2015. Darwin Core RDF guide. Biodiversity Information Standards (TDWG). <http://rs.tdwg.org/dwc/terms/guides/rdf/2021-07-15>
## 1 Introduction (non-normative)
@ -1335,7 +1335,7 @@ term | domain | range
dcterms:modified | --- | rdfs:Literal[^1]
dcterms:bibliographicCitation | dcterms:BibliographicResource | rdfs:Literal
[^1]: Recommended format is [ISO 8601:2004(E)](http://en.wikipedia.org/wiki/ISO_8601). See notes on date terms in [Section 3.4](#34-terms-defined-by-darwin-core-that-are-expected-to-be-used-only-with-literal-values-normative) for further information.
[^1]: Recommended format is [ISO 8601-1:2019](http://en.wikipedia.org/wiki/ISO_8601). See notes on date terms in [Section 3.4](#34-terms-defined-by-darwin-core-that-are-expected-to-be-used-only-with-literal-values-normative) for further information.
### 3.3 Imported Dublin Core terms that have non-literal objects and corresponding terms that have literal objects (normative)
@ -1364,11 +1364,11 @@ dcterms:bibliographicCitation | dcterms:BibliographicResource | rdfs:Literal
Darwin Core term | Notes on expressing as RDF
--- | ---
`dwc:eventDate`<br>`dwc:georeferencedDate`<br>`dwc:dateIdentified`<br>`dwc:relationshipEstablishedDate`<br>`dwc:measurementDeterminedDate` | These date terms have range `rdfs:Literal`[^8]. Best practice as specified in the term definition recommends that they should be formatted according to [ISO 8601:2004(E)](https://en.wikipedia.org/wiki/ISO_8601). There is no defined [XML Schema datatype](https://www.w3.org/TR/xmlschema11-2/) that corresponds exactly to ISO 8601:2004(E), therefore the entire set of possible values cannot be specified using an `rdf:datatype` attribute. The [XML Schema dateTime datatype](https://www.w3.org/TR/xmlschema11-2/#dateTime) (`xsd:dateTime`) which is effectively a subset of ISO 8601:2004(E), may be used as an `rdf:datatype` attribute. However, `xsd:dateTime` requires the complete series of year, month, day, hour, second (e.g., 002-10-10T12:00:00) and does not permit listing only part of this hierarchy (e.g., only the year) as is allowed in ISO 8601:2004(E).
`dwc:eventTime` | It is recommended that the format described by [ISO 8601:2004(E)](https://en.wikipedia.org/wiki/ISO_8601) be used. As with the date terms, there is no [XML Schema datatype](https://www.w3.org/TR/xmlschema11-2/) that includes all of the possible values allowed in ISO 8601:2004(E), so there is no generic `rdf:datatype` attribute that would apply to all possible instances. The [XML Schema dateTime datatype](https://www.w3.org/TR/xmlschema11-2/#dateTime) (`xsd:time`) which is effectively a subset of ISO 8601:2004(E) may be used as an `rdf:datatype` attribute although it is limited to values that include hours, minutes, and seconds (e.g., 13:07:56-05:00).
`dwc:individualCount`<br>`dwc:decimalLatitude`<br>`dwc:decimalLongitude`<br>`dwc:coordinatePrecision`<br>`dwc:pointRadiusSpatialFit`<br>`dwc:coordinateUncertaintyInMeters`<br>`dwc:minimumElevationInMeters`<br>`dwc:maximumElevationInMeters`<br>`dwc:minimumDepthInMeters`<br>`dwc:maximumDepthInMeters`<br>`dwc:minimumDistanceAboveSurfaceInMeters`<br>`dwc:maximumDistanceAboveSurfaceInMeters`<br>`dwc:startDayOfYear`<br>`dwc:endDayOfYear`<br>`dwc:year`<br>`dwc:month`<br>`dwc:day`<br>`dwc:footprintSpatialFit`<br>`dwc:measurementValue`<br>`dwc:measurementAccuracy` | These terms are expected to have literal values that are numeric. Therefore, an `rdf:datatype` attribute describing the form of the number should be used.
`dwc:eventDate`<br>`dwc:georeferencedDate`<br>`dwc:dateIdentified`<br>`dwc:relationshipEstablishedDate`<br>`dwc:measurementDeterminedDate` | These date terms have range `rdfs:Literal`[^8]. Best practice as specified in the term definition recommends that they should be formatted according to [ISO 8601-1:2019](https://en.wikipedia.org/wiki/ISO_8601). There is no defined [XML Schema datatype](https://www.w3.org/TR/xmlschema11-2/) that corresponds exactly to ISO 8601-1:2019, therefore the entire set of possible values cannot be specified using an `rdf:datatype` attribute. The [XML Schema dateTime datatype](https://www.w3.org/TR/xmlschema11-2/#dateTime) (`xsd:dateTime`) which is effectively a subset of ISO 8601-1:2019, may be used as an `rdf:datatype` attribute. However, `xsd:dateTime` requires the complete series of year, month, day, hour, second (e.g., 002-10-10T12:00:00) and does not permit listing only part of this hierarchy (e.g., only the year) as is allowed in ISO 8601-1:2019.
`dwc:eventTime` | It is recommended that the format described by [ISO 8601-1:2019](https://en.wikipedia.org/wiki/ISO_8601) be used. As with the date terms, there is no [XML Schema datatype](https://www.w3.org/TR/xmlschema11-2/) that includes all of the possible values allowed in ISO 8601-1:2019, so there is no generic `rdf:datatype` attribute that would apply to all possible instances. The [XML Schema dateTime datatype](https://www.w3.org/TR/xmlschema11-2/#dateTime) (`xsd:time`) which is effectively a subset of ISO 8601-1:2019 may be used as an `rdf:datatype` attribute although it is limited to values that include hours, minutes, and seconds (e.g., 13:07:56-05:00).
`dwc:individualCount`<br>`dwc:decimalLatitude`<br>`dwc:decimalLongitude`<br>`dwc:coordinatePrecision`<br>`dwc:pointRadiusSpatialFit`<br>`dwc:coordinateUncertaintyInMeters`<br>`dwc:minimumElevationInMeters`<br>`dwc:maximumElevationInMeters`<br>`dwc:minimumDepthInMeters`<br>`dwc:maximumDepthInMeters`<br>`dwc:minimumDistanceAboveSurfaceInMeters`<br>`dwc:maximumDistanceAboveSurfaceInMeters`<br>`dwc:startDayOfYear`<br>`dwc:endDayOfYear`<br>`dwc:year`<br>`dwc:month`<br>`dwc:day`<br>`dwc:footprintSpatialFit`<br>`dwc:measurementAccuracy` | These terms are expected to have literal values that are numeric. Therefore, an `rdf:datatype` attribute describing the form of the number should be used.
`dwc:occurrenceRemarks`<br>`dwc:eventRemarks`<br>`dwc:locationRemarks`<br>`dwc:georeferenceRemarks`<br>`dwc:identificationRemarks`<br>`dwc:taxonRemarks`<br>`dwc:organismRemarks`<br>`dwc:relationshipRemarks`<br>`dwc:measurementRemarks` | Because these are remarks, they are expected to have literal values with an `xml:lang` attribute.
`dwc:catalogNumber`<br>`dwc:samplingEffort`<br>`dwc:organismName`<br>`dwc:verbatimEventDate`<br>`dwc:verbatimLocality`<br>`dwc:verbatimElevation`<br>`dwc:verbatimCoordinates`<br>`dwc:verbatimLatitude`<br>`dwc:verbatimLongitude`<br>`dwc:verbatimDepth`<br>`dwc:verbatumTaxonRank` | Based on their term definitions, these terms are expected to have untyped literal values
`dwc:catalogNumber`<br>`dwc:samplingEffort`<br>`dwc:organismName`<br>`dwc:verbatimIdentification`<br>`dwc:verbatimEventDate`<br>`dwc:verbatimLocality`<br>`dwc:verbatimElevation`<br>`dwc:verbatimCoordinates`<br>`dwc:verbatimLatitude`<br>`dwc:verbatimLongitude`<br>`dwc:verbatimDepth`<br>`dwc:verbatumTaxonRank` | Based on their term definitions, these terms are expected to have untyped literal values.
`dwc:otherCatalogNumbers` | There is no simple mapping because of the kinds of identifiers people use and variety of relationships that there may be among identifiers. For non-IRI identifiers expressed as string values, the string may be provided as a literal value of `dwc:otherCatalogNumbers`. Whether this is preferable to providing multiple `dwc:catalogNumber` properties may depend on community practice. `owl:sameAs` may be used to associate other IRI identifiers with the subject IRI if that is appropriate.
`dwc:basisOfRecord` | Use only with literal value strings consisting of the local name component of Darwin Core class IRIs. Use `rdf:type` to refer to IRIs that describe the type of the resource.
`dwc:dynamicProperties` | Expected to contain JSON as a literal. Communities of practice might choose to use other vocabularies or develop their own vocabularies to express this sort of content directly as RDF.
@ -1382,7 +1382,7 @@ See [Section 2.7](#27-darwin-core-convenience-terms-non-normative) for more info
Darwin Core term | Notes
--- | ---
`dwc:collectionCode`<br>`dwc:institutionCode`<br>`dwc:ownerInstitutionCode` | The subject resource can be any resource that is part of a collection. As an alternative, use the object property `dwciri:inCollection` to link the subject resource to an IRI for the collection containing the institution that owns or controls the resource.
`dwc:kingdom`<br>`dwc:phylum`<br>`dwc:class`<br>`dwc:order`<br>`dwc:family`<br>`dwc:genus`<br>`dwc:subgenus`<br>`dwc:specificEpithet`<br>`dwc:infraspecificEpithet`<br>`dwc:higherClassification`<br>`dwc:vernacularName`<br>`dwc:nameAccordingTo`<br>`dwc:scientificName`<br>`dwc:taxonRank`<br>`dwc:scientificNameAuthorship`<br>`dwc:nomenclaturalStatus`<br>`dwc:namePublishedIn`<br>`dwc:namePublishedInYear`<br>`dwc:nomenclaturalCode`<br>`dwc:originalNameUsage`<br>`dwc:taxonomicStatus`<br>`dwc:parentNameUsage`<br>`dwc:acceptedNameUsage` | The subject resource should be a `dwc:Identification` instance. See [Section 2.7.4](#274-description-of-a-taxonomic-entity-normative) for a discussion of why it not recommended to use these as properties of `dwc:Taxon` instances. As an alternative, use the object property `dwciri:toTaxon` to link the subject `dwc:Identification` instance to a taxonomic entity such as a taxon, taxon concept, or taxon name use. It is likely that these taxonomic entities will have a complex structure which differentiates among name entities, name strings, application of a name to a concept, which expresses parent/child and set relationships among entities, and which tracks provenance information about the names, references, and concepts. The flat nature of text-based Darwin Core cannot represent such a complex structure and it is beyond the scope of this guide to describe them.
`dwc:kingdom`<br>`dwc:phylum`<br>`dwc:class`<br>`dwc:order`<br>`dwc:family`<br>`dwc:subfamily`<br>`dwc:genus`<br>`dwc:genericName`<br>`dwc:subgenus`<br>`dwc:infragenericEpithet`<br>`dwc:specificEpithet`<br>`dwc:infraspecificEpithet`<br>`dwc:cultivarEpithet`<br>`dwc:higherClassification`<br>`dwc:vernacularName`<br>`dwc:nameAccordingTo`<br>`dwc:scientificName`<br>`dwc:taxonRank`<br>`dwc:scientificNameAuthorship`<br>`dwc:nomenclaturalStatus`<br>`dwc:namePublishedIn`<br>`dwc:namePublishedInYear`<br>`dwc:nomenclaturalCode`<br>`dwc:originalNameUsage`<br>`dwc:taxonomicStatus`<br>`dwc:parentNameUsage`<br>`dwc:acceptedNameUsage` | The subject resource should be a `dwc:Identification` instance. See [Section 2.7.4](#274-description-of-a-taxonomic-entity-normative) for a discussion of why it not recommended to use these as properties of `dwc:Taxon` instances. As an alternative, use the object property `dwciri:toTaxon` to link the subject `dwc:Identification` instance to a taxonomic entity such as a taxon, taxon concept, or taxon name use. It is likely that these taxonomic entities will have a complex structure which differentiates among name entities, name strings, application of a name to a concept, which expresses parent/child and set relationships among entities, and which tracks provenance information about the names, references, and concepts. The flat nature of text-based Darwin Core cannot represent such a complex structure and it is beyond the scope of this guide to describe them.
`dwc:higherGeography`<br>`dwc:continent`<br>`dwc:waterBody`<br>`dwc:islandGroup`<br>`dwc:island`<br>`dwc:countryCode`<br>`dwc:country`<br>`dwc:stateProvince`<br>`dwc:county`<br>`dwc:municipality`<br>`dwc:locality` | The subject resource should be a `dcterms:Location` instance. As an alternative, use the object property `dwciri:inDescribedPlace` to link the subject resource to a standardized place described as part of a hierarchy. See [Section 2.7.5](#275-names-of-geographic-subdivisions-normative) for details. It is likely that providers will want to provide a text value for `dwc:locality` even if `dwciri:inDescribedPlace` is used to replace the other hierarchical convenience terms in this category. This is because it is unlikely that a place description at this most specific level (e.g., "15 km N of Essen") would be represented by a standardized IRI-identified place instance. There is no `dwciri:` analogue of `dwc:locality` because if an IRI-identified place were available to represent the locality, the term `dwciri:inDescribedPlace` would be used to link to it.
`dwc:earliestEonOrLowestEonothem`<br>`dwc:latestEonOrHighestEonothem`<br>`dwc:earliestEraOrLowestErathem`<br>`dwc:latestEraOrHighestErathem`<br>`dwc:earliestPeriodOrLowestSystem`<br>`dwc:latestPeriodOrHighestSystem`<br>`dwc:earliestEpochOrLowestSeries`<br>`dwc:latestEpochOrHighestSeries`<br>`dwc:earliestAgeOrLowestStage`<br>`dwc:latestAgeOrHighestStage` | The subject resource should be a `dwc:GeologicalContext` instance. As an alternative, use the object properties `dwciri:earliestGeochronologicalEra` and `dwciri:latestGeochronologicalEra` as described in [Section 3.6](#36-dwciri-terms-having-local-names-that-dont-correspond-to-terms-in-the-dwc-darwin-core-namespace-normative). See [Section 2.7.6](#276-chronostratographic-geological-timescale-descriptors-normative) for details.
`dwc:lithostratigraphicTerms`<br>`dwc:group`<br>`dwc:formation`<br>`dwc:member`<br>`dwc:bed` | The subject resource should be a `dwc:GeologicalContext` instance. As an alternative, use the object property `dwciri:fromLithostratigraphicUnit` to link the subject resource to the lowest appropriate unit of a lithostratigraphic hierarchy.
@ -1405,7 +1405,7 @@ Darwin Core term having a `dwciri:` analogue with the same local name | Notes on
`dwc:recordedBy`<br>`dwc:identifiedBy`<br>`dwc:georeferencedBy`<br>`dwc:measurementDeterminedBy` | The object is an agent; use a well-known IRI such as those referenced in the list of sources of controlled values in the [Darwin Core informative ancillary web page](https://github.com/tdwg/rdf/blob/master/DwCAncillary.md).
`dwc:locationAccordingTo` | The object is an agent or publication. Use a well-known IRI when possible, such as an HTTP-proxied DOI.
`dwc:georeferenceProtocol`<br>`dwc:georeferenceSources`<br>`dwc:samplingProtocol` | The object is a published or well-known reference; use an IRI version (preferably HTTP proxied) of doi, isbn, issn, etc. if available.
`dwc:sex`<br>`dwc:lifeStage`<br>`dwc:reproductiveCondition`<br>`dwc:establishmentMeans`<br>`dwc:behavior`<br>`dwc:occurrenceStatus`<br>`dwc:disposition`<br>`dwc:verbatimCoordinateSystem`<br>`dwc:verbatimSRS`<br>`dwc:geodeticDatum`<br>`dwc:georeferenceVerificationStatus`<br>`dwc:footprintWKT`<br>`dwc:footprintSRS`<br>`dwc:lowestBiostratigraphicZone`<br>`dwc:highestBiostratigraphicZone`<br>`dwc:identificationVerificationStatus`<br>`dwc:identificationQualifier`<br>`dwc:preparations`<br>`dwc:typeStatus`<br>`dwc:measurementType`<br>`dwc:measurementUnit`<br>`dwc:measurementMethod` | Recommended best practice is to use a controlled vocabulary if one is available.
`dwc:sex`<br>`dwc:lifeStage`<br>`dwc:reproductiveCondition`<br>`dwc:establishmentMeans`<br>`dwc:behavior`<br>`dwc:occurrenceStatus`<br>`dwc:disposition`<br>`dwc:verbatimCoordinateSystem`<br>`dwc:verbatimSRS`<br>`dwc:geodeticDatum`<br>`dwc:verticalDatum`<br>`dwc:georeferenceVerificationStatus`<br>`dwc:footprintWKT`<br>`dwc:footprintSRS`<br>`dwc:lowestBiostratigraphicZone`<br>`dwc:highestBiostratigraphicZone`<br>`dwc:identificationVerificationStatus`<br>`dwc:identificationQualifier`<br>`dwc:preparations`<br>`dwc:typeStatus`<br>`dwc:measurementType`<br>`dwc:measurementValue`<br>`dwc:measurementUnit`<br>`dwc:measurementMethod` | Recommended best practice is to use a controlled vocabulary if one is available.
`dwc:informationWithheld`<br>`dwc:dataGeneralizations`<br>`dwc:habitat` | If the object property (`dwciri:` analogue) is used rather than the `dwc:` property, the object property should point to a stable resource which might be a controlled vocabulary.
`dwc:fieldNumber`<br>`dwc:fieldNotes` | `dwciri:fieldNumber` is an object property whose subject is a (possibly IRI-identified) resource that is the field notes and whose object is a `dwc:Event` instance. `dwciri:fieldNotes` is an object property whose subject is a `dwc:Event` instance and whose object is a (possibly IRI-identified) resource that is the field notes.
`dwc:recordNumber` | `dwciri:recordNumber` is an object property whose subject is an occurrence and whose object is a (possibly IRI-identified) resource that is the field notes.
@ -1417,4 +1417,14 @@ Darwin Core term | Notes
`dwc:relationshipOfResource`<br>`dwc:relationshipAccordingTo` | The non-RDF use of terms organized under the `dwc:ResourceRelationship` class depends on values for `dwc:resourceID` and `dwc:relatedResourceID`, terms which cannot be used in RDF for reasons discussed in [Section 2.6](#26-darwin-core-id-terms-and-rdf-normative). As of November 2014, the RDF/OWL Task Group is seeking a way to express resource relationships as RDF. For the present, `dwciri:` analogues have not been adopted for these two terms. See the [Darwin Core informative ancillary web page](https://github.com/tdwg/rdf/blob/master/DwCAncillary.md) for further discussion.
`dwc:associatedOccurrences`<br>`dwc:associatedMedia`<br>`dwc:associatedSequences`<br>`dwc:associatedTaxa`<br>`dwc:associatedOrganisms` | Use `dcterms:relation` and `rdf:type`, or terms that indicate more specific relationships as described in [Section 2.8](#28-darwin-core-association-terms-non-normative) (Darwin Core association terms).
`dwc:previousIdentifications` | There is no consensus object property for associating identifications with resources of other classes. From whatever scheme you have chosen to provide object properties, use same object property as used for the most recent identification but provide an earlier dwc:dateIdentified value.
`dwc:organismScope` | Use `rdf:type` with a non-literal object. See the comment at http://rs.tdwg.org/dwc/terms/organismScope.
`dwc:organismScope` | Use `rdf:type` with a non-literal object. See the comment at <http://rs.tdwg.org/dwc/terms/organismScope>.
### 3.9 Chronometric Age extension `chrono:` terms that have analogues in the `chronoiri:` namespace (normative)
The [Chronometric Age vocabulary](http://rs.tdwg.org/dwc/doc/chrono/) extends the core Darwin Core vocabulary. It has a second namespace for IRI-valued terms, `chronoiri:`, which operates analogously to the `dwciri:` namespace.
Chronometric Age term having a `chronoiri:` analogue with the same local name | Notes on the `chronoiri:` analogues
--- | ---
`chrono:chronometricAgeDeterminedBy` | The object is an agent; use a well-known IRI such as those referenced in the list of sources of controlled values in the [Darwin Core informative ancillary web page](https://github.com/tdwg/rdf/blob/master/DwCAncillary.md).
`chrono:chronometricAgeConversionProtocol`<br>`chrono:chronometricAgeProtocol`<br>`chrono:chronometricAgeUncertaintyMethod` | The object is a published or well-known reference; use an IRI version (preferably HTTP proxied) of doi, isbn, issn, etc. if available.
`chrono:earliestChronometricAgeReferenceSystem`<br>`chrono:latestChronometricAgeReferenceSystem`<br>`chrono:materialDated` | Recommended best practice is to use a controlled vocabulary if one is available.