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ObjectGroup - Review and update examples for all 'types of thing' properties #463

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essvee opened this issue Mar 17, 2023 · 7 comments
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Class:ObjectGroup easy-win Small, standalone change that usually only affects a single file review Changes to be made following feedback from internal reviewers

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@essvee
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essvee commented Mar 17, 2023

See meeting notes: 16th March 23
Original defs:

Current master defs: https://github.com/tdwg/cd/blob/review/standard/terms/ltc_standard_terms_draft.csv#L135
See also: the 'types of thing' tab in the working spreadsheet.

The examples we have in place for these fields (esp objectType and preparationType) are outdated relative to the term defs and should be reviewed + fixed before they confuse everyone unnecessarily. Make sure that every example is valid for the term it's being used against.

@essvee essvee added review Changes to be made following feedback from internal reviewers update after review labels Mar 17, 2023
@essvee essvee added easy-win Small, standalone change that usually only affects a single file and removed update after review labels Apr 6, 2023
@jbstatgen jbstatgen self-assigned this Apr 6, 2023
jbstatgen added a commit that referenced this issue Apr 6, 2023
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jbstatgen commented Apr 6, 2023

baseTypeOfCollection #365

Updated examples to "MaterialEntity, InformationArtefact, AbstractConcept"

Changed MaterialSample to MaterialEntity following the proposal by the Material Sample task group.

Added AbstractConcept for eg. standards, models, controlled vocabularies, etc.

Changed "High-level term" to "High-level terms" in the definition, reason: can be an array.

In the Notes: changed "occurrences" to "material entities".

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jbstatgen commented Apr 6, 2023

typeOfCollection: #255 (added JuB 6.4.23)

Modified definition: removing "...that exist ..." so that it is now "Additional information that describes the object(s) in the collection."

Added to Notes: "High-level information that enables the finding of the group and/or its object(s) in searches by users on the web using attributes commonly of interest. Recommended best practice is to use a controlled vocabulary. ..."

Updated examples to

if baseTypeOfCollection = MaterialEntity: Living, Preserved, Fossilized, Non-biological, Human-made;
if baseTypeOfCollection = InformationArtefact: Digital, Physical

Originally:
"PreservedSpecimens, FossilSpecimens, MineralSpecimens, ArchaeologicalArtefacts, EthnographicObjects, HumanRemains, HominidRemains, MaterialSamples, LivingSpecimens"
[HumanObservations, MachineObservations]

Removed "Specimens" following discussions in the Material Sample task group.

HumanObservations, MachineObservations: They should become part of a vocabulary under InformationArtefact for property samplingProcess

ArchaeologicalArtefacts, EthnographicObjects: They become part of Human-made

HumanRemains, HominidRemains: These are questionable, are they needed? They should be found via Anthropology, Medical/Biomedical and/or Paleontology under a Discipline classification

jbstatgen added a commit that referenced this issue Apr 6, 2023
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preservationMode: #321

Modified notes to:
"This property should be only used in association with ObjectGroups that contain paleontological material. It is aligned with the concept of preservationMode in ABCD(EFG) (https://efg.geocase.eu/documentation/html/efg.html#element_PreservationMode_Link03032878)."

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jbstatgen commented Apr 11, 2023

objectType: #304

In Examples: changed

  • "tissue, specimen, culture, rna, mineral, dna, environmental sample, HTS Library" to "if baseTypeOfCollection = MaterialEntity: Specimen, Tissue, Culture, HTS Library, Lysate, Environmental sample (e.g. eDNA), Extracted/Preserved DNA/RNA, Microscope slide, Spore print, Macrofossil, Mesofossil, Microfossil, Oversized fossil, Macro-object, Micro-object, Oversized object, Cut/polished gemstone, Core, Fluid, Hazardous material/object, Mixed; if typeOfCollection = Human-made: bowl, textile; if baseTypeOfCollection = InformationArtefact: Text, Audio, Visual"

In Notes: changed

  • "This should not be used for classifying objects by taxon. The best way to do that is to use the Taxon class (formal taxonomy and vernacular names) or ObjectClassification class (informal classification). For cultural collections terms such as 'bowl', 'textile' are appropriate at this level. For large collections of multiple types use pipe delimited lists."
  • to "This should not be used for classifying objects by taxon. The best way to do that is to use the Taxon class (formal taxonomy and vernacular names) or ObjectClassification class (informal classification)."
    (removed "For large collections of multiple types use pipe delimited lists." and removed "For cultural collections terms such as 'bowl', 'textile' are appropriate at this level.")

In Notes: added
"Hands-on, practical attributes classifying the stored curated objects. You will expect to find these kinds and types of objects when you go to and access their storage location. ..."

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jbstatgen commented Apr 12, 2023

preparationType: #64

Notes: changed

  • Added "These attributes commonly identify the parts or states that are the outcome of the preparation process, which produced the curated object. ..."
  • Removed from end of Notes: "For large collections with multiple types use a pipe delimited list."
  • Added " For cultural collections terms such as 'bowl', 'textile' are appropriate at this level."

Updated Examples to

  • "if objectType = Specimen or Part of entity: Bones, Eggs, Pollen, Muscle, Leaf, Blood, Skins, Shells, Wood, ... ; if objectType = culture: cell culture, axenic culture, viable cells; if typeOfCollection = human-made: Bowl, Textile, ...; etc"
  • Removed "if objectType = culture: cell culture, axenic culture, viable cells; " since these terms are now part of the vocabulary of preservationMethod

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jbstatgen commented Apr 12, 2023

material: #261

Notes changed:

  • Added ". The object, or artefact could contain biological parts, for example jewellery made of amber with insects in, or cloaks made of bird feathers. "

Examples changed:

  • Removed "Examples include terms such as brick, gold, aluminium, polycarbonate, resin, amber, feather"
  • Added "Biological body, Organism material (cp. objectType = Organism product), Viable cells, Protein, RNA, DNA, etc."

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jbstatgen commented Apr 12, 2023

preservationMethod: #65

Notes changed:

  • Removed "If the collection has multiple preservationMethods then this should be expressed elsewhere, such as in ObjectQuantity. "
  • Added "Preservation method generally describes the final storage state. ..."

Examples changed to
"dried, dried_pressed, dried_pinned, Dried assemblage, Dried - not assembled, Dry preserved, papered/packaged, slide box, Skeletonized, Tanned, mounted, Slide mount, Embedded, gum_arabic, Blood sampling cards (biomedical), Fluid preserved, Alcohol, formaledhyde, glycerin, EDTA, frozen / cryopreserved, Cryopreserved / frozen - 80C, refrigerated, freeze_dried, Surface coating, SEM stub, Stasis, cell culture, axenic culture, viable cells, Controlled atmosphere, Climate controlled conditions, Non climate controlled conditions, no_treatment, etc."

@essvee essvee closed this as completed May 31, 2023
magpiedin added a commit that referenced this issue Oct 19, 2023
* Adds hasObject properties to termlist and updates examples

* Adds datatypes to termlist

* updates identifier to identifierValue

* adds Event.eventName

* specifies array item datatypes

* add range & class-level-properties

* Updates Person.Identifier examples to have more than one

* Create ltc_skos_mapping.csv

Initial version of skos mappings

* Create Latimer Core browser.pbix

New version of LtC browser

* Update Latimer Core browser.pbix

Changed skos mapping csv source from local to GitHub

* Update Latimer Core browser.pbix

Minor fix to property html

* Update ltc_standard_terms_draft.csv

Added term_status, term_added and term_modified

* Update ltc_standard_terms_draft.csv

Added proposed hasSchemeTerm and hasSchemeMeasurementOrFact properties to the CollectionDescriptionScheme class

* Update ltc_standard_terms_draft.csv

Added proposed hasObjectGroup property to CollectionDescriptionScheme class

* Update ltc_standard_terms_draft.csv

Removed objectClassificationParent property, as superseded by the hasObjectClassification property

* Update ltc_skos_mapping.csv

Tweaks to some mapping relations, and also removed duplicate rows (repeated for hasIdentifier etc in mulltiple classes)

* Update ltc_standard_terms_draft.csv

Updates from SKOS mapping review (see issues #399 to #412)

* Updates json schema and examples: removes objectClassificationParent and renames Identifier.source as .identifierSource

* updates schema description

* Adds PersonRole.hasMeasurementOrFact

* Fixes omission of parent class in termlist.csv

* Updates termlist and schema

* Adds term to termlist.csv

* Updates StorageLocation schema to include locationDescription

* Adds ObjectGroup.alternativeCollectionName to termlist.

* Adds ObjectGroup.alternativeCollectionName to ObjectGroup schema and example files

* Fixes a couple of typos

* adds object count estimates to orgClass

* Separates property datatypes from normative termlist fields

* Updates bool property names in class-level examples

* Updates bool property names in json schema files

* Updates bool property names, labels and defs

* Small, pedantic edits to definitions to match those in the termlist

* updates collectionDescriptionScheme term name to hasCollectionDescriptionScheme

* Adds GO terms to skos mapping

* Adds GO terms to termlist

* Adds GO terms to datatypes list

* Adds GeographicOrigin.ecoRegion

* Updates json schema with amended definitions for GeoOrigin terms

* Update ltc_standard_terms_draft.csv

Fixed some special character encodings

* Update Latimer Core browser.pbix

Refreshed data from termlists

* kw-csv-to-json (#432)

* setup csv-to-json in tools

* setup json-schema converter

* add first batch of test-output

* draft update 'required'/minItems for arrays

* add env options for live/test output

* add initial test-output

* fix link?

* update how-to

* edit trouble-shooting + to-do

* generalize variable names

* fix link

* fix name

* fix description

* typo

* reorganize

* fix link

* update minItems/requirements & troubleshooting

* auto-json (#433)

* fix MeasOrFact

* note date-datatype (to-do)

* update main json-schema

* Revert "auto-json (#433)" (#439)

This reverts commit d881331.

* Add spec csv-to-json tool (#440)

* add test-spec based on ltc terms CSV

* edit test-spec based on ltc terms CSV

* add SPEC_CSV variable to .env

* add spec script + output path

* require CollStHis:hasMeasOrFact and GeoCtxt:bed

* fix spec script's use of spec-csv

* revert to pre-auto JSON

* fix repeatable term vs class

* fix SPEC_CSV example URL

* add spec JSON_OUTPUT_PATH

* add missing spec-steps

* fix typo

* re-try auto-generating json-schema (#441)

* Update ltc_standard_terms_draft.csv

Fixed mislabeled measurementAccuracy term

* Added Role class

Added the new Role class, removed PersonRole.role and added hasRole, with some tweaks to PersonRole class notes

* Updated Role mappings and datatypes

Also modified PersonRole.hasRole to repeatable array

* Adds country codes to examples field

* add note to Address.addressCountry field

relates to #455

* Update to notes field: only for paleo OGs

#465

* Updated examples to "`MaterialEntity`, `InformationArtefact`, `AbstractConcept`"

#463

* Removes contactDetailType and adds additional examples to contactDetailFunction

* Adds ContactDetail.contactDetailFunction

* Update of typeOfCollection?

#463

* Adds ObjectClassification.isTopParent

* Adds hasParentEvent to Event

* Updated typeOfCollection

#463

* Update ltc_standard_terms_draft.csv

* Corrects required/repeatable flags for ObjectGroup.alternativeCollectionName

* baseTypeOfCollection: change from term to terms in def

#365

* Updated typeOfCollection example from "MaterialEntities" to "MaterialEntity"

#255

* Update typeOfCollection examples

* Updated objectType

#304

* objectType: example update

#304

* objectType: removed spelling error

#304

* Updated preparationType Examples and Notes

* Updated Examples of preparationType

#64

* Changed examples of material

#261

* Corrected spelling mistake in material

#261

* Updated examples for preparationType

#64

* Updated Notes and Examples of preservationMethod

#65

* Update to Notes in baseTypeOfCollection

#365

* rename CollectionDescriptionScheme

...to ObjectGroupDescriptionScheme - #429

* rename CollectionDescriptionScheme

...to ObjectGroupDescriptionScheme - #429

* rename remaining CollectionDescriptionScheme

to "ObjectGroupDescriptionScheme" - #429

* baseTypeOfCollection: set repeatable = YES

#446

* Updated baseTypeOfCollection: spelling error

#446

* rename to LatimerCoreScheme

following #476 & updated #429

* Update ltc_standard_terms_draft.csv

Updated according to issue #462

* Update ltc_standard_terms_draft.csv

Updated with additional notes from issue #450

* rename baseTypeOfCollection

...to baseTypeOfObjectGroup - #477

* rename typeOfCollection

to typeOfObjectGroup - #478

* rename to LatimerCoreScheme - #429

#429

* rename baseTypeOfCollection - #477

to baseTypeOfObjectGroup

* rename typeOfCollection - #478

to typeOfObjectGroup

* rename typeOfCollection - #478

to typeOfObjectGroup

* rename CollectionDescriptionScheme - #429

to LatimerCoreScheme

* Add files via upload

Terms defined as human versus machine readable. Check terms after all review updates are made.

* update LtCScheme in ranges - #429

* rename CDScheme to LtCScheme - #429

"CollectionDescriptionScheme" class name updated to "LatimerCoreScheme"

* rename typeOfCollection in ltc.csv - #478

...to typeOfObjectGroup

* rename baseTypeOfCollection in ltc.csv - #477

...to baseTypeOfObjectGroup

* Updated GeographicOrigin to GeographicContext

* Update ltc_standard_terms_draft.csv

Further updates to definitions in the renamed GeographicContext class

* Updates class-level notes and usage recommendations

* Removes reference to stratigraphy from verbatimChronometricAge

* Update ltc_standard_terms_draft.csv

Changed labels for stateProvince and county #431

* Update ltc_categories.csv

Updated GeographicContext name & definition

* Updated hasOrganisationalUnit to hasParentOrganisationalUnit

* updates examples for chronometricAgeProtocol

* updates baseTypeOfObjectGroup to array

* updates usage notes for isDerivedCollection

* update CDScheme to LtCScheme in termlist-header

* Updated example for Reference.referenceDetails

#454 326

* 2nd Example added for Reference.referenceDetails

#326

* Updated example: collection dynamics to growth status

#367

* Updated example 

#124

* Removes collectionDescriptionPID and adds recommendation to hasIdentifier

* extends TemporalCoverage to PersonRole, changes dates to datetimes

* Update ltc_standard_terms_draft.csv

added superGroup property

* Updated referenceText to referenceName

Closes #453

* Changed collectionName to required = No

Closes #485

* Updates GeographicContext.ecoRegion notes

* Update ltc_datatypes.csv

Updated remaining references to GeographicOrigin to GeographicContext

* Added new EcologicalContext class

Add class and term definitions

* Update ltc_standard_terms_draft.csv

Removed ResourceRelationship.resourceRelationshipID as superseded by hasIdentifier

* Update ltc_standard_terms_draft.csv

Removed GeographicContext.salinityType as superseded by EcologicalContext class

* Update ltc_standard_terms_draft.csv

While checking boolean values: for "isDistinctObjects" removed "If isDistinctObjects is set to 'true', then no collection object should be covered by more than one object group within the LatimerCoreScheme." from "Usage", since it was already present in "Notes" and fits better there.

* Update ltc.csv

changed 1 of 11 instances of Organization... to Organisation. The other 10 are from other standards.

* Update ltc_standard_terms_draft.csv

2 of 4 instances of "organiza..." replaced with "organisa..." The other 2 are namespace dependent.

* match readme to master

to prevent conflicts

* Update Latimer Core browser.pbix

Refreshed from term list, added icon and other minor tweaks

* Refreshed derived csvs fpr terms

Regenerated namespace-specific CSVs and category CSVs from main term CSV

* clean up examples in ltc_standard_terms_draft.csv

* Update Latimer Core browser.pbix

* Added SKOS mapping decision tree

* Term updates from new SKOS review

Tweaks to terms to get definitions in line with the outcomes of the new SKOS mappings review. Includes namespace changes and definition tweaks. Also added new StorageLocation.hasParentStorageLocation term.

* Update ltc_standard_terms_draft.csv

Fix to hasParentStorageLocation term name

* Update ltc_standard_terms_draft.csv

Removed escaped double quotes

* Update ltc_standard_terms_draft.csv

Removed unpaired double quote

* Update ltc_standard_terms_draft.csv

* Update ltc_standard_terms_draft.csv

* Update ltc_standard_terms_draft.csv

* Updated term mappings

Updated SKOS mappings after review and replacing term names with URIs. Added more comprehensive SSSOM mappings.

* Removed trailing CSV columns

* Update Latimer Core browser.pbix

Refreshed data and modified to accept SKOS mappings from URIs

* Update ltc_standard_terms_draft.csv

Fixed issues with merge overwriting changes

* Update Latimer Core browser.pbix

Refreshed data

---------

Co-authored-by: Kate Webbink <[email protected]>
Co-authored-by: Matt Woodburn <[email protected]>
Co-authored-by: jbstatgen <[email protected]>
Co-authored-by: fmjjones <[email protected]>
Co-authored-by: Sharon Grant <[email protected]>
Co-authored-by: Kate Webbink <[email protected]>
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