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Merge pull request #341 from gaiaresources/BDRSPS-1045
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BDRSPS-1045 Move `dwc:catalogNumber` and `dwc:collectionCode` to the `dwc:Occurrence` node
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@joecrowleygaia
joecrowleygaia authored Nov 20, 2024
2 parents f76e0ee + 66e11e0 commit be28437
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4 changes: 2 additions & 2 deletions ...ates/incidental_occurrence_data_v3/examples/margaret_river_flora/margaret_river_flora.csv
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Expand Up @@ -11,7 +11,7 @@ providerRecordID,providerRecordIDSource,locality,decimalLatitude,decimalLongitud
10,WAM,Cowaramup Bay Road,-33.86,115.02,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Caladenia excelsa,,Stream Environment and Water Pty Ltd,,Caladenia excelsa,,,,Plantae,,,,,,,,
11,WAM,Cowaramup Bay Road,-33.86,115.02,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Caladenia ?excelsa,,Stream Environment and Water Pty Ltd,,Caladenia excelsa,?,One unopened flower when recorded and one leaf only. ID not confirmed,,Plantae,,,,,,,,
12,WAM,,-33.8,115.21,WGS84,,,26/09/2019,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,Caladenia excelsa,,,,Plantae,,,,,,,,
13,WAM,Cowaramup Bay Road,-33.86,115.02,WGS84,,,26/09/2019,,,PreservedSpecimen,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,CC123,WAM,,,,,,,,,Stream Environment and Water Pty Ltd,,Caladenia excelsa,,,,Plantae,,,,,,,,
14,WAM,Cowaramup Bay Road,-33.86,115.02,WGS84,20,Coordinates rounded to the nearest 10 km for conservation concern,26/09/2019,,,HumanObservation,Stream Environment and Water Pty Ltd,,,,,,,5,individuals,,,,,,,CC456,WAM,,,,,,,Caladenia ?excelsa,,Stream Environment and Water Pty Ltd,,Caladenia excelsa,?,Could not confirm the ID due to damaged flower,,Plantae,,,,,,,,
13,WAM,Cowaramup Bay Road,-33.86,115.02,WGS84,,,26/09/2019,,,PreservedSpecimen,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,C01,CC123,WAM,,,,,,,,,Stream Environment and Water Pty Ltd,,Caladenia excelsa,,,,Plantae,,,,,,,,
14,WAM,Cowaramup Bay Road,-33.86,115.02,WGS84,20,Coordinates rounded to the nearest 10 km for conservation concern,26/09/2019,,,HumanObservation,Stream Environment and Water Pty Ltd,,,,,,,5,individuals,,,,,,C01,CC456,WAM,,,,,,,Caladenia ?excelsa,,Stream Environment and Water Pty Ltd,,Caladenia excelsa,?,Could not confirm the ID due to damaged flower,,Plantae,,,,,,,,
8022FSJMJ079c5cf,WAM,Cowaramup Bay Road,-33.8,115.21,WGS84,50,Coordinates rounded to the nearest 10 km for conservation concern,26/09/2019,,human observation,PreservedSpecimen,Stream Environment and Water Pty Ltd,PE:12:8832,present,"Closed forest of Melaleuca lanceolata. White, grey or brown sand, sandy loam.",native,Dried out leaf tips,2,,,adult,male,No breeding evident,MR-456,Stream Environment and Water Pty Ltd,32237,ARACH,WAM,BHP2012-7521 | M12378,BHP,Wet (in ethanol or some other preservative),26/09/2019,https://www.ncbi.nlm.nih.gov/nuccore/MH040669.1 | https://www.ncbi.nlm.nih.gov/nuccore/MH040616.1,Sanger dideoxy sequencing,Caladenia ?excelsa,2019-09-27T12:34+08:00,Stream Environment and Water Pty Ltd,Visually identified in the field (sighting),Caladenia excelsa,species incerta,no flowers present,Caladenia excelsa Hopper & A.P.Br.,Plantae,species,VU,WA,Check against Threatened and Priority Fauna List WA available from https://www.dpaw.wa.gov.au/plants-and-animals/threatened-species-and-communities/threatened-animals. Last updated 13 June 2022,,WA-BIO,,
ABC123,WAM,Cowaramup Bay Road,-33.8,115.21,WGS84,30,Coordinates generalised,26/09/2019,,new sampling protocol,new basis of record,Stream Environment and Water Pty Ltd,PE:12:8833,new occurrence status,new habitat,new establishment means,Leaves brown,6,,,new life stage,new sex,new reproductiveCondition,MR-457,Stream Environment and Water Pty Ltd,32238,ARACH,WAM,BHP2012-7522 | M12379,BHP,new preparations,27/09/2019,https://www.ncbi.nlm.nih.gov/nuccore/MH040669.1 | https://www.ncbi.nlm.nih.gov/nuccore/MH040616.1,new sequencing method,Caladenia ?excelsa,2019-09-27T12:34+08:00,Stream Environment and Water Pty Ltd,new identification method,Caladenia excelsa,new identification qualifier,new remarks,Caladenia excelsa Hopper & A.P.Br.,new kingdom,new taxon rank,new threat status,WA,a random selection,,,Category 1,The Department of Biodiversity and Conservation
102 changes: 36 additions & 66 deletions ...ates/incidental_occurrence_data_v3/examples/margaret_river_flora/margaret_river_flora.ttl
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Expand Up @@ -15,7 +15,7 @@
<http://createme.org/OccurrenceCollection/basisOfRecord/HumanObservation> a schema:Collection ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
schema:identifier "Occurrence Collection - Basis Of Record - HumanObservation" ;
schema:member <http://createme.org/sample/specimen/14> ;
schema:member <http://createme.org/occurrence/14> ;
tern:hasAttribute <http://createme.org/attribute/basisOfRecord/HumanObservation> .

<http://createme.org/OccurrenceCollection/basisOfRecord/PreservedSpecimen> a schema:Collection ;
Expand Down Expand Up @@ -573,19 +573,6 @@
sosa:observedProperty <http://linked.data.gov.au/def/tern-cv/05cbf534-c233-4aa8-a08c-00b28976ed36> ;
sosa:usedProcedure <http://linked.data.gov.au/def/tern-cv/ea1d6342-1901-4f88-8482-3111286ec157> .

<http://createme.org/observation/specimen/verbatimIdentification/14> a tern:Observation ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
rdfs:comment "verbatimID-observation" ;
time:hasTime [ a time:Instant ;
rdfs:comment "Date unknown, template eventDateStart used as proxy" ;
time:inXSDDate "2019-09-26"^^xsd:date ] ;
prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
sosa:hasFeatureOfInterest <http://createme.org/sample/specimen/14> ;
sosa:hasResult <http://createme.org/result/specimen/verbatimIdentification/Caladenia-excelsa> ;
sosa:hasSimpleResult "Caladenia ?excelsa" ;
sosa:observedProperty <http://linked.data.gov.au/def/tern-cv/70646576-6dc7-4bc5-a9d8-c4c366850df0> ;
sosa:usedProcedure <http://linked.data.gov.au/def/tern-cv/2eef4e87-beb3-449a-9251-f59f5c07d653> .

<http://createme.org/observation/specimen/verbatimIdentification/8022FSJMJ079c5cf> a tern:Observation ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
rdfs:comment "verbatimID-observation" ;
Expand Down Expand Up @@ -649,6 +636,19 @@
sosa:observedProperty <http://linked.data.gov.au/def/tern-cv/70646576-6dc7-4bc5-a9d8-c4c366850df0> ;
sosa:usedProcedure <http://linked.data.gov.au/def/tern-cv/2eef4e87-beb3-449a-9251-f59f5c07d653> .

<http://createme.org/observation/verbatimIdentification/14> a tern:Observation ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
rdfs:comment "verbatimID-observation" ;
time:hasTime [ a time:Instant ;
rdfs:comment "Date unknown, template eventDateStart used as proxy" ;
time:inXSDDate "2019-09-26"^^xsd:date ] ;
prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
sosa:hasFeatureOfInterest <http://createme.org/occurrence/14> ;
sosa:hasResult <http://createme.org/result/verbatimIdentification/Caladenia-excelsa> ;
sosa:hasSimpleResult "Caladenia ?excelsa" ;
sosa:observedProperty <http://linked.data.gov.au/def/tern-cv/70646576-6dc7-4bc5-a9d8-c4c366850df0> ;
sosa:usedProcedure <http://linked.data.gov.au/def/tern-cv/2eef4e87-beb3-449a-9251-f59f5c07d653> .

<http://createme.org/observation/verbatimIdentification/2> a tern:Observation ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
rdfs:comment "verbatimID-observation" ;
Expand Down Expand Up @@ -1359,10 +1359,13 @@
rdf:value "Caladenia excelsa Hopper & A.P.Br." ;
tern:featureType <http://example.com/concept/acceptedNameUsage> .

<http://createme.org/result/specimen/verbatimIdentification/Caladenia-excelsa> a tern:Text,
tern:Value ;
rdf:value "Caladenia ?excelsa" .

<http://createme.org/sample/specimen/13> a tern:FeatureOfInterest,
tern:Sample ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
dwc:catalogNumber "CC123"^^<https://linked.data.gov.au/dataset/bdr/datatypes/catalogNumber/WAM> ;
rdfs:comment "specimen-sample" ;
sosa:isResultOf <http://createme.org/sampling/specimen/13> ;
sosa:isSampleOf <http://createme.org/occurrence/13> ;
Expand Down Expand Up @@ -1403,21 +1406,9 @@
sosa:hasResult <http://createme.org/sample/specimen/13> ;
sosa:usedProcedure <http://linked.data.gov.au/def/tern-cv/7930424c-f2e1-41fa-9128-61524b67dbd5> .

<http://createme.org/sampling/specimen/14> a tern:Sampling ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
geo:hasGeometry _:Nfc9ba55a50d500211c02e20000000003 ;
geo:hasMetricSpatialAccuracy 2e+01 ;
rdfs:comment "specimen-sampling" ;
time:hasTime [ a time:Instant ;
rdfs:comment "Date unknown, template eventDateStart used as proxy" ;
time:inXSDDate "2019-09-26"^^xsd:date ] ;
sosa:hasFeatureOfInterest <http://createme.org/occurrence/14> ;
sosa:hasResult <http://createme.org/sample/specimen/14> ;
sosa:usedProcedure <http://linked.data.gov.au/def/tern-cv/7930424c-f2e1-41fa-9128-61524b67dbd5> .

<http://createme.org/sampling/specimen/8022FSJMJ079c5cf> a tern:Sampling ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
geo:hasGeometry _:Nfc9ba55a50d500211c02e20000000005 ;
geo:hasGeometry _:Nfc9ba55a50d500211c02e20000000003 ;
geo:hasMetricSpatialAccuracy 5e+01 ;
rdfs:comment "specimen-sampling" ;
time:hasTime [ a time:Instant ;
Expand All @@ -1428,7 +1419,7 @@

<http://createme.org/sampling/specimen/ABC123> a tern:Sampling ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
geo:hasGeometry _:Nfc9ba55a50d500211c02e20000000007 ;
geo:hasGeometry _:Nfc9ba55a50d500211c02e20000000005 ;
geo:hasMetricSpatialAccuracy 3e+01 ;
rdfs:comment "specimen-sampling" ;
time:hasTime [ a time:Instant ;
Expand Down Expand Up @@ -1482,28 +1473,10 @@
rdf:value "Boronia anceps" ;
tern:featureType <http://example.com/concept/scientificName> .

<http://createme.org/result/specimen/verbatimIdentification/Caladenia-excelsa> a tern:Text,
tern:Value ;
rdf:value "Caladenia ?excelsa" .

<http://createme.org/result/verbatimIdentification/Boronia-anceps> a tern:Text,
tern:Value ;
rdf:value "Boronia anceps" .

<http://createme.org/result/verbatimIdentification/Caladenia-excelsa> a tern:Text,
tern:Value ;
rdf:value "Caladenia ?excelsa",
"Caladenia excelsa" .

<http://createme.org/sample/specimen/14> a tern:FeatureOfInterest,
tern:Sample ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
dwc:catalogNumber "CC456"^^<https://linked.data.gov.au/dataset/bdr/datatypes/catalogNumber/WAM> ;
rdfs:comment "specimen-sample" ;
sosa:isResultOf <http://createme.org/sampling/specimen/14> ;
sosa:isSampleOf <http://createme.org/occurrence/14> ;
tern:featureType <http://linked.data.gov.au/def/tern-cv/2e122e23-881c-43fa-a921-a8745f016ceb> .

<http://createme.org/occurrence/1> a dwc:Occurrence,
tern:FeatureOfInterest ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
Expand Down Expand Up @@ -1648,9 +1621,16 @@
tern:Value ;
rdf:value "Banksia sessilis var. cordata" .

<http://createme.org/result/verbatimIdentification/Caladenia-excelsa> a tern:Text,
tern:Value ;
rdf:value "Caladenia ?excelsa",
"Caladenia excelsa" .

<http://createme.org/occurrence/13> a dwc:Occurrence,
tern:FeatureOfInterest ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
dwc:catalogNumber "CC123"^^<https://linked.data.gov.au/dataset/bdr/datatypes/catalogNumber/WAM> ;
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:spatial _:N489292b7f1191795326ddd2200000024 ;
Expand All @@ -1663,6 +1643,8 @@
<http://createme.org/occurrence/14> a dwc:Occurrence,
tern:FeatureOfInterest ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
dwc:catalogNumber "CC456"^^<https://linked.data.gov.au/dataset/bdr/datatypes/catalogNumber/WAM> ;
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:spatial _:N489292b7f1191795326ddd2200000027 ;
Expand All @@ -1675,8 +1657,6 @@
<http://createme.org/sample/specimen/8022FSJMJ079c5cf> a tern:FeatureOfInterest,
tern:Sample ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
dwc:catalogNumber "ARACH"^^<https://linked.data.gov.au/dataset/bdr/datatypes/catalogNumber/WAM> ;
dwc:collectionCode "32237" ;
rdfs:comment "specimen-sample" ;
sosa:isResultOf <http://createme.org/sampling/specimen/8022FSJMJ079c5cf> ;
sosa:isSampleOf <http://createme.org/occurrence/8022FSJMJ079c5cf> ;
Expand All @@ -1685,8 +1665,6 @@
<http://createme.org/sample/specimen/ABC123> a tern:FeatureOfInterest,
tern:Sample ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
dwc:catalogNumber "ARACH"^^<https://linked.data.gov.au/dataset/bdr/datatypes/catalogNumber/WAM> ;
dwc:collectionCode "32238" ;
rdfs:comment "specimen-sample" ;
sosa:isResultOf <http://createme.org/sampling/specimen/ABC123> ;
sosa:isSampleOf <http://createme.org/occurrence/ABC123> ;
Expand All @@ -1703,6 +1681,8 @@
<http://createme.org/occurrence/8022FSJMJ079c5cf> a dwc:Occurrence,
tern:FeatureOfInterest ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
dwc:catalogNumber "ARACH"^^<https://linked.data.gov.au/dataset/bdr/datatypes/catalogNumber/WAM> ;
dwc:collectionCode "32237" ;
prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
sosa:usedProcedure <http://linked.data.gov.au/def/tern-cv/ea1d6342-1901-4f88-8482-3111286ec157> ;
schema:identifier "BHP2012-7521"^^<https://linked.data.gov.au/dataset/bdr/datatypes/catalogNumber/BHP>,
Expand All @@ -1719,6 +1699,8 @@
<http://createme.org/occurrence/ABC123> a dwc:Occurrence,
tern:FeatureOfInterest ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
dwc:catalogNumber "ARACH"^^<https://linked.data.gov.au/dataset/bdr/datatypes/catalogNumber/WAM> ;
dwc:collectionCode "32238" ;
prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
sosa:usedProcedure <http://createme.org/bdr-cv/methods/samplingProtocol/new-sampling-protocol> ;
schema:identifier "BHP2012-7522"^^<https://linked.data.gov.au/dataset/bdr/datatypes/catalogNumber/BHP>,
Expand Down Expand Up @@ -1896,26 +1878,18 @@
rdf:subject <http://createme.org/sampling/specimen/13> ;
rdfs:comment "supplied as" .

[] a rdf:Statement ;
geo:hasGeometry [ a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.86 115.02)"^^geo:wktLiteral ] ;
rdf:object _:Nfc9ba55a50d500211c02e20000000003 ;
rdf:predicate geo:hasGeometry ;
rdf:subject <http://createme.org/sampling/specimen/14> ;
rdfs:comment "supplied as" .

[] a rdf:Statement ;
geo:hasGeometry [ a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.8 115.21)"^^geo:wktLiteral ] ;
rdf:object _:Nfc9ba55a50d500211c02e20000000005 ;
rdf:object _:Nfc9ba55a50d500211c02e20000000003 ;
rdf:predicate geo:hasGeometry ;
rdf:subject <http://createme.org/sampling/specimen/8022FSJMJ079c5cf> ;
rdfs:comment "supplied as" .

[] a rdf:Statement ;
geo:hasGeometry [ a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.8 115.21)"^^geo:wktLiteral ] ;
rdf:object _:Nfc9ba55a50d500211c02e20000000007 ;
rdf:object _:Nfc9ba55a50d500211c02e20000000005 ;
rdf:predicate geo:hasGeometry ;
rdf:subject <http://createme.org/sampling/specimen/ABC123> ;
rdfs:comment "supplied as" .
Expand Down Expand Up @@ -1984,14 +1958,10 @@ _:Nfc9ba55a50d500211c02e20000000001 a geo:Geometry ;
rdfs:comment "Location unknown, location of field sampling used as proxy" .

_:Nfc9ba55a50d500211c02e20000000003 a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.86 115.02)"^^geo:wktLiteral ;
rdfs:comment "Location unknown, location of field sampling used as proxy" .

_:Nfc9ba55a50d500211c02e20000000005 a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.8 115.21)"^^geo:wktLiteral ;
rdfs:comment "Location unknown, location of field sampling used as proxy" .

_:Nfc9ba55a50d500211c02e20000000007 a geo:Geometry ;
_:Nfc9ba55a50d500211c02e20000000005 a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.8 115.21)"^^geo:wktLiteral ;
rdfs:comment "Location unknown, location of field sampling used as proxy" .

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