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vernacularNames in Opmerkingen, not matching GBIF_Code/Soort #51

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PietrH opened this issue Aug 7, 2023 · 3 comments
Open

vernacularNames in Opmerkingen, not matching GBIF_Code/Soort #51

PietrH opened this issue Aug 7, 2023 · 3 comments
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mapping question Further information is requested

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@PietrH
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PietrH commented Aug 7, 2023 •
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The raw data reports species "Lettersierschildpad" with the correct gbif id, however in Opmerkingen there is mention of : 12/06: sabotage, 07/07: Zaagrugschildpad ( groot exemplaar), which is Graptemys sp.

This event has been in the dataset for a while, occurrences in current output:

type language license rightsHolder datasetID institutionCode datasetName basisOfRecord eventID occurrenceID recordedBy organismQuantity organismQuantityType occurrenceStatus samplingProtocol samplingEffort eventDate countryCode municipality verbatimLatitude verbatimLongitude verbatimCoordinateSystem verbatimSRS decimalLatitude decimalLongitude geodeticDatum coordinateUncertaintyInMeters scientificName kingdom taxonRank
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 428110 RATO 2 individual(s) present cage trap 1 cage trap 2023-05-19 13:07:41 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 430568 RATO 2 individual(s) present cage trap 1 cage trap 2023-05-22 11:42:24 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 437818 RATO 2 individual(s) present cage trap 1 cage trap 2023-05-26 10:42:52 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 438973 RATO 2 individual(s) present cage trap 1 cage trap 2023-05-30 08:42:31 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 444885 RATO 2 individual(s) present cage trap 1 cage trap 2023-06-02 09:20:24 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 446113 RATO 2 individual(s) present cage trap 1 cage trap 2023-06-05 10:13:53 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 451724 RATO 2 individual(s) present cage trap 1 cage trap 2023-06-08 12:47:56 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 455180 RATO 2 individual(s) present cage trap 1 cage trap 2023-06-12 13:00:05 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 462626 RATO 2 individual(s) present cage trap 1 cage trap 2023-06-19 11:20:37 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 471851 RATO 2 individual(s) present cage trap 1 cage trap 2023-06-26 12:25:41 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 477783 RATO 2 individual(s) present cage trap 1 cage trap 2023-06-30 13:48:12 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 487067 RATO 2 individual(s) present cage trap 1 cage trap 2023-07-07 13:04:32 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 492257 RATO 2 individual(s) present cage trap 1 cage trap 2023-07-14 20:23:27 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species
Event en http://creativecommons.org/publicdomain/zero/1.0/ RATO https://doi.org/10.15468/fw2rbx RATO RATO - Daily operations commissioned by the province East Flanders, Belgium HumanObservation 41583 498235 RATO 2 individual(s) present cage trap 1 cage trap 2023-07-24 09:38:24 BE Gent 198323.4 109641.6 Lambert coordinates Belgian Datum 1972 51.09361 3.79266 WGS84 30 Trachemys scripta Animalia species

In the raw data we can see only the last 3 records make mention of Graptemys sp.
image

There are probably more examples of vernacular names being mentioned in Opmerkingen, some of which might also not match the GBIF_Code provided.

For now, I will not make an exception and parse just these records to add a new species, but I'll create an issue to be discussed when everyone involved is back from holidays.

Originally posted by @PietrH in #50 (comment)
@PietrH PietrH added the mapping label Aug 7, 2023
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PietrH commented Aug 7, 2023

Repeatable with:

raw_data <- readr::read_csv(
  here::here("data", "raw", "rato_data.csv")
filter(raw_data, Dossier_ID == 41583)

@PietrH
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PietrH commented Aug 7, 2023

@LienReyserhove

In some records, there are dutch vernacular names in Opmerkingen, for example:

"12/06: sabotage, 07/07: Zaagrugschildpad ( groot exemplaar)"

in occurrenceID: 498235

This is mapped to a different turtle, based on the GBIF id. I believe they were trying to catch 2 individuals of species a, but caught 1 of a and one of b. The data however shows this as 2 of a

Do I understand this correctly? How would you handle this? Should this be fixed on the data side, should we make an exception just for this record in the mapping

Do you think we should systematically check for vernacular and scientific names in Opmerkingen that don't match the GBIF_Code as part of the tests?

@PietrH
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PietrH commented Aug 7, 2023

Same table as above, but less columns:

Dossier_ID OBJECTID Dossier_Status Soort Waarneming Actie Opmerkingen Laatst_Bewerkt_Datum
41583 428110 Opvolging Lettersierschildpad Vastgesteld (aantal) = 2; NA NA 2023-05-19 13:07:41
41583 430568 Opvolging Lettersierschildpad Vastgesteld (aantal) = 2; NA NA 2023-05-22 11:42:24
41583 437818 Opvolging Lettersierschildpad Vastgesteld (aantal) = 2; Vangst (aantal) = 1; NA 2023-05-26 10:42:52
41583 438973 Opvolging Lettersierschildpad Vastgesteld (aantal) = 2; NA NA 2023-05-30 08:42:31
41583 444885 Opvolging Lettersierschildpad Vastgesteld (aantal) = 2; NA NA 2023-06-02 09:20:24
41583 446113 Opvolging Lettersierschildpad Vastgesteld (aantal) = 2; NA NA 2023-06-05 10:13:53
41583 451724 Opvolging Lettersierschildpad Vastgesteld (aantal) = 2; NA NA 2023-06-08 12:47:56
41583 455180 Opvolging Lettersierschildpad Vastgesteld (aantal) = 2; NA 12/06: sabotage 2023-06-12 13:00:05
41583 462626 Opvolging Lettersierschildpad Vastgesteld (aantal) = 2; NA 12/06: sabotage 2023-06-19 11:20:37
41583 471851 Opvolging Lettersierschildpad Vastgesteld (aantal) = 2; NA 12/06: sabotage 2023-06-26 12:25:41
41583 477783 Opvolging Lettersierschildpad Vastgesteld (aantal) = 2; NA 12/06: sabotage 2023-06-30 13:48:12
41583 487067 Opvolging Lettersierschildpad Vastgesteld (aantal) = 2; Vangst (aantal) = 1; 12/06: sabotage, 07/07: Zaagrugschildpad ( groot exemplaar) 2023-07-07 13:04:32
41583 492257 Opvolging Lettersierschildpad Vastgesteld (aantal) = 2; NA 12/06: sabotage, 07/07: Zaagrugschildpad ( groot exemplaar) 2023-07-14 20:23:27
41583 498235 Verwerkt en afgesloten Lettersierschildpad Vastgesteld (aantal) = 2; NA 12/06: sabotage, 07/07: Zaagrugschildpad ( groot exemplaar) 2023-07-24 09:38:24

@PietrH PietrH added the question Further information is requested label Aug 7, 2023
@PietrH PietrH mentioned this issue Aug 7, 2023
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