Review (#498)

* 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CollectionDescriptionScheme class * Update ltc_standard_terms_draft.csv Removed objectClassificationParent property, as superseded by the hasObjectClassification property * Update ltc_skos_mapping.csv Tweaks to some mapping relations, and also removed duplicate rows (repeated for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]>
tdwg · Oct 19, 2023 · a756830 · a756830
1 parent af6991f
commit a756830
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diff --git a/.gitignore b/.gitignore
@@ -1 +1,5 @@
 .DS_Store
+.env
+.pylintrc
+.vscode
+venv
diff --git a/examples/class-level json examples/address-example.json b/examples/class-level json examples/address-example.json
@@ -5,16 +5,16 @@
     "addressLocality": "Chicago",
     "addressRegion": "Illinois",
     "addressCountry": "United States",
-    "identifier":
+    "hasIdentifier":
     [
         {
             "identifierType": "what3words",
-            "identifier": "cages.potato.kinds"
+            "identifierValue": "cages.potato.kinds"
         },
         {
             "identifierType": "ISO 3166-1 alpha-2 country code",
-            "identifier": "US",
-            "source": "ISO"
+            "identifierValue": "US",
+            "identifierSource": "ISO"
         }
     ]
 }
diff --git a/examples/class-level json examples/collection-description-scheme-example.json b/examples/class-level json examples/collection-description-scheme-example.json
@@ -1,15 +1,15 @@
 {
     "basisOfScheme": "Institutional holdings",
-    "distinctObjects": true,
+    "isDistinctObjects": true,
     "schemeName": "Institutional Registry Project",
-    "identifier":
+    "hasIdentifier":
     [
         {
             "identifierType": "LtC Schema ID",
-            "identifier": "0000-0000-0000-0000"
+            "identifierValue": "0000-0000-0000-0000"
         }
     ],
-    "reference":
+    "hasReference":
     [
         {
             "referenceType": "Website",

diff --git a/examples/class-level json examples/collection-status-history-example.json b/examples/class-level json examples/collection-status-history-example.json
@@ -1,21 +1,21 @@
 {
     "statusType": "Stewardship",
     "status": "active",
-    "temporalCoverage":
+    "hasTemporalCoverage":
     [
         {
             "temporalCoverageStartDate": "1846-08-10",
-            "reference":
+            "hasReference":
             [
                 {
                     "referenceType": "Digitised Document",
                     "referenceText": "Act establishing the Smithsonian Institution",
                     "referenceDetails": "Marc Rothenberg, ed. The Papers of Joseph Henry, The Princeton Years, January 1844 - December 1846, vol. 6. Washington, D.C.: Smithsonian Institution Press, p. 463.",
                     "resoureURI": "https://www.si.edu/object/siris_sic_12522",
-                    "identifier":
+                    "hasIdentifier":
                     [
                         {
-                            "identifier": "siris_sic_12522",
+                            "identifierValue": "siris_sic_12522",
                             "identifierType": "Smithsonian Libraries and Archives Object ID"
                         }
                     ]

diff --git a/examples/class-level json examples/event-example.json b/examples/class-level json examples/event-example.json
@@ -1,23 +1,24 @@
 {
     "verbatimEventDate": "1755-1756",
     "habitat": "temperate rainforest",
-    "personRole":
+    "eventName": "Cloudland Expedition (1755-1756)",
+    "hasPersonRole":
     [
         {
             "role": "Collector",
             "startedAtTime": "1755-09-01",
-            "person":
+            "hasPerson":
             [
                 {
                     "fullName": "Anne Monson",
                     "familyName": "Monson",
                     "givenName": "Anne",
-                    "identifier":
+                    "hasIdentifier":
                     [
                         {
                             "identifierType": "URI",
                             "identifierSource": "https://www.wikidata.org/wiki/",
-                            "identifier": "Q15994645"
+                            "identifierValue": "Q15994645"
                         }
                     ]
                 }
@@ -26,7 +27,7 @@
         {
             "role": "Navigator",
             "startedAtTime": "1755-09-01",
-            "person":
+            "hasPerson":
             [
                 {
                     "fullName": "Sidney Smith",
@@ -36,7 +37,7 @@
             ]
         }
     ],
-    "measurementOrFact":
+    "hasMeasurementOrFact":
     [
         {
             "measurementType": "Object Count",

diff --git a/examples/class-level json examples/geographic-origin-example.json b/examples/class-level json examples/geographic-origin-example.json
@@ -6,15 +6,15 @@
     "countryCode": "AU",
     "salinityType": "marine",
     "stateProvince": "Queensland",
-    "identifiers":
+    "hasIdentifier":
     [
         {
-            "identifierType": "GeoNames ID",
-            "source": "https://www.geonames.org/",
-            "identifier": 2146841
+            "identifierType": "URI",
+            "identifierSource": "https://www.geonames.org/",
+            "identifierValue": "2146841"
         }
     ],
-    "measurementOrFact":
+    "hasMeasurementOrFact":
     [
         {
             "measurementType": "decimal latitude",

diff --git a/examples/class-level json examples/identifier-example.json b/examples/class-level json examples/identifier-example.json
@@ -1,4 +1,4 @@
 {
     "identifierType": "Acronym",
-    "identifier": "EMNH"
+    "identifierValue": "EMNH"
 }
diff --git a/examples/class-level json examples/measurement-or-fact-example.json b/examples/class-level json examples/measurement-or-fact-example.json
@@ -4,18 +4,18 @@
     "measurementAccuracy": "Estimate",
     "measurementMethod": "DiSSCo MIDS level",
     "measurementDerivation": "Reported",
-    "reference":
+    "hasReference":
     [
         {
             "referenceType": "Measurement methodology",
             "resourceURI": "https://doi.org/10.5281/zenodo.3465285",
             "referenceDetails": "Saarenmaa, Hannu, Agosti, Donat, Dillen, Mathias, Egloff, Willi, Gagnier, Pierre-Yves, Groom, Quentin, Hardisty, Alex, & Raes, Niels. (2019). Open access implementation guidelines for DiSSCo. Deliverable D6.5 (pp. 1–35).",
             "referenceText": "Open access implementation guidelines for DiSSCo. Deliverable D6.5",
-            "identifier":
+            "hasIdentifier":
             [
                 {
                     "identifierType": "DOI",
-                    "identifier": "10.5281/zenodo.3465285"
+                    "identifierValue": "10.5281/zenodo.3465285"
                 }
             ]
         }

diff --git a/examples/class-level json examples/object-classification-example.json b/examples/class-level json examples/object-classification-example.json
@@ -1,11 +1,9 @@
 {
     "objectClassificationName": "Arachnids",
-    "objectClassificationParent": "Insects",
-    "objectClassification":
+    "hasObjectClassification":
     [
         {
             "objectClassificationName": "Insects",
-            "objectClassificationParent": "Invertebrates"
         },
         {
             "objectClassificationName": "Invertebrates"