BDRSPS-1109 When surveyID is missing from an occurrence, treat it as …

…incidental i.e. don't link it to a Survey in the RDF output.
gaiaresources · Dec 13, 2024 · 358ee26 · 358ee26
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diff --git a/...emplates/survey_occurrence_data_v3/examples/margaret_river_flora/margaret_river_flora.ttl b/...emplates/survey_occurrence_data_v3/examples/margaret_river_flora/margaret_river_flora.ttl
@@ -1464,8 +1464,7 @@
 <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/occurrence/12> a dwc:Occurrence,
         tern:FeatureOfInterest ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc575500000021 ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1488,8 +1487,7 @@
         tern:FeatureOfInterest ;
     prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc575500000000 ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1501,8 +1499,7 @@
         tern:FeatureOfInterest ;
     prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc57550000001b ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1514,8 +1511,7 @@
         tern:FeatureOfInterest ;
     prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc57550000001e ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1527,8 +1523,7 @@
         tern:FeatureOfInterest ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
     schema:identifier "PE:12:8831" ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc575500000003 ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1540,8 +1535,7 @@
         tern:FeatureOfInterest ;
     prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Test-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc575500000006 ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1553,8 +1547,7 @@
         tern:FeatureOfInterest ;
     prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc575500000009 ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1566,8 +1559,7 @@
         tern:FeatureOfInterest ;
     prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc57550000000c ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1579,8 +1571,7 @@
         tern:FeatureOfInterest ;
     prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc57550000000f ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1592,8 +1583,7 @@
         tern:FeatureOfInterest ;
     prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc575500000012 ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1605,8 +1595,7 @@
         tern:FeatureOfInterest ;
     prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc575500000015 ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1618,8 +1607,7 @@
         tern:FeatureOfInterest ;
     prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc575500000018 ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1650,8 +1638,7 @@
     dwc:collectionCode "C01" ;
     prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc575500000024 ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1665,8 +1652,7 @@
     dwc:collectionCode "C01" ;
     prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:N7bfc9936b099cf9353fc575500000027 ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;
@@ -1739,9 +1725,6 @@
     tern:featureType <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/bdr-cv/featureType/occurrence/kingdom/new-kingdom> ;
     tern:locationDescription "Cowaramup Bay Road" .
 
-<https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> a tern:Survey ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> .
-
 <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> a prov:Agent ;
     schema:name "Stream Environment and Water Pty Ltd" .
 

diff --git a/abis_mapping/templates/survey_occurrence_data_v3/examples/organism_qty.ttl b/abis_mapping/templates/survey_occurrence_data_v3/examples/organism_qty.ttl
@@ -51,9 +51,6 @@
     schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     tern:featureType <http://linked.data.gov.au/def/tern-cv/5bf7ae21-a454-440b-bdd7-f2fe982d8de4> .
 
-<https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> a tern:Survey ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> .
-
 <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/attribution/Gaia-Resources/resourceProvider> a prov:Attribution ;
     prov:agent <https://linked.data.gov.au/dataset/bdr/orgs/Gaia-Resources> ;
     prov:hadRole <https://linked.data.gov.au/def/data-roles/resourceProvider> .
@@ -79,8 +76,7 @@
         tern:FeatureOfInterest ;
     sosa:isSampleOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Site/P1> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
-    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000>,
-        <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000/Survey/1> ;
+    schema:isPartOf <https://linked.data.gov.au/dataset/bdr/00000000-0000-0000-0000-000000000000> ;
     schema:spatial _:Nb0c3d4fa822b88b4d3f8743700000000 ;
     schema:temporal [ a time:TemporalEntity ;
             time:hasBeginning [ a time:Instant ;

diff --git a/abis_mapping/templates/survey_occurrence_data_v3/mapping.py b/abis_mapping/templates/survey_occurrence_data_v3/mapping.py
@@ -544,9 +544,12 @@ def apply_mapping_row(
 
         # Create URIs for Survey-related fields (i.e. fields not on the incidental template)
 
-        # Create TERN survey IRI from surveyID field
+        # Create TERN survey IRI from surveyID field, only when it is provided
         survey_id: str | None = row["surveyID"]
-        survey = utils.iri_patterns.survey_iri(base_iri, survey_id)
+        if survey_id:
+            survey = utils.iri_patterns.survey_iri(base_iri, survey_id)
+        else:
+            survey = None
 
         # Create Tern Site IRI, depending on the siteID field
         site_id: str | None = row["siteID"]
@@ -4244,7 +4247,7 @@ def add_sensitivity_category_collection(
 
     def add_survey(
         self,
-        uri: rdflib.URIRef,
+        uri: rdflib.URIRef | None,
         dataset: rdflib.URIRef,
         graph: rdflib.Graph,
     ) -> None:
@@ -4257,6 +4260,9 @@ def add_survey(
             dataset: The dataset URI
             graph: The graph to update
         """
+        if uri is None:
+            return
+
         # Add type
         graph.add((uri, a, utils.namespaces.TERN.Survey))
         # Add dataset link
@@ -4302,7 +4308,7 @@ def add_occurrence(
         other_catalog_numbers_datatype: rdflib.URIRef | None,
         catalog_number_datatype: rdflib.URIRef | None,
         provider_recorded_by: rdflib.URIRef | None,
-        survey: rdflib.URIRef,
+        survey: rdflib.URIRef | None,
         site: rdflib.URIRef | None,
         site_visit: rdflib.URIRef | None,
         dataset: rdflib.URIRef,
@@ -4457,8 +4463,9 @@ def add_occurrence(
             # Add to Graph
             graph.add((uri, utils.namespaces.DWC.collectionCode, rdflib.Literal(row["collectionCode"])))
 
-        # Add survey
-        graph.add((uri, rdflib.SDO.isPartOf, survey))
+        # Add survey, if provided
+        if survey:
+            graph.add((uri, rdflib.SDO.isPartOf, survey))
 
         # Add site if provided
         if site is not None:

diff --git a/abis_mapping/templates/survey_occurrence_data_v3/schema.json b/abis_mapping/templates/survey_occurrence_data_v3/schema.json
@@ -720,7 +720,7 @@
     {
       "name": "surveyID",
       "title": "Survey ID",
-      "description": "The identifier of the Survey that the occurrence comes from. This field should be completed if it is ambiguous as to which survey the occurrence belongs to.",
+      "description": "The identifier of the Survey that the Occurrence comes from. If this field is left blank, the Occurrence will be treated as incidental.",
       "example": "AR220-01",
       "type": "string",
       "format": "default",

diff --git a/abis_mapping/templates/survey_occurrence_data_v3/templates/instructions.md b/abis_mapping/templates/survey_occurrence_data_v3/templates/instructions.md
@@ -103,6 +103,7 @@ Changes from Systematic Survey Occurrence Data Template v2.0.0
 
 * When [`surveyID`](#surveyID-field) is provided, it must have a value that matches a `surveyID`
   in the Systematic Survey Metadata template to indicate which Survey the Occurrence belongs to.
+  When [`surveyID`](#surveyID-field) is blank, the Occurrence will be treated as incidental.
 
 ## APPENDICES
 ### APPENDIX-I: Vocabulary List