Darwin Core mapping for occurrence dataset

type

occurrence %<>% mutate(type = "Event")

modified

language

occurrence %<>% mutate(language = "en")

license

occurrence %<>% mutate(license = "http://creativecommons.org/publicdomain/zero/1.0/")

rightsHolder

occurrence %<>% mutate(rightsHolder = "Ghent University Aquatic Ecology")

accessRights

occurrence %<>% mutate(accessRights = "http://www.inbo.be/en/norms-for-data-use")

bibliographicCitation

references

institutionID

collectionID

datasetID

occurrence %<>% mutate(datasetID = "https://doi.org/10.15468/xjtfoo")

institutionCode

occurrence %<>% mutate(institutionCode = "INBO")

collectionCode

datasetName

occurrence %<>% mutate(datasetName = "Alien macroinvertebrates in Flanders, Belgium")

ownerInstitutionCode

basisOfRecord

occurrence %<>% mutate(basisOfRecord = "HumanObservation")

informationWithheld

dataGeneralizations

dynamicProperties

occurrenceID

Checking whether occurrenceID is a unique code (TRUE)

n_distinct(occurrence $ raw_taxon_occurrence_comment) == nrow(occurrence)

## [1] TRUE

mapping:

occurrence %<>% mutate(occurrenceID = raw_taxon_occurrence_comment)

catalogNumber

recordNumber

recordedBy

give all unique name/group/organization records in raw_survey_event_comment (base column for recordedBy and identifiedBy)

occurrence %>% select (raw_survey_event_comment) %>%
  distinct(raw_survey_event_comment) %>%
  arrange (raw_survey_event_comment) %>%
  kable()

replace these records by a (list of) person(s), in the recommended best format for recordedBy

occurrence %<>% mutate (
  recordedBy = recode (raw_survey_event_comment,
                       "2004_KreeftenBBICalc_Warmoes" = "Warmoes T", 
                       "VMM, 2004_KreeftenBBICalc_Warmoes" = " ",
                       "2004_niet_BBICacl - Warmoes" = " ",
                       "Claudio Salvo" = "Salvo C",
                       "D'udekem D'Acoz" = "d'Udekem d'Acoz",
                       "databank VMM" = "VMM",
                       "Dirk en Walda Hennebel" = "Hennebel D | Hennebel W",
                       "eigen data VMM" = "VMM",
                       "extra stalen" = "Boets P",
                       "Frank de Block-Burij" = "de Block-Burij F",
                       "Geert Vanloot" = "Vanloot G",
                       "Gérard" = "Gérard",
                       "Gérard, 1986" = "Gérard",
                       "Gunter Flipkens" = "Flipkens G",
                       "Hans de Blauwe" = "de Blauwe H",
                       "Herwig Mees" = "Mees H",
                       "IRSNB-Karel Wouters, 2002" = "Wouters K",
                       "Johan Auwerx" = "Auwerx J",
                       "Joost Mertens" = "Mertens J",
                       "Kobe Janssen" = "Janssen K",
                       "koen" = "Lock K",
                       "Koen Maes" = "Maes K",
                       "Leloup L." = "Leloup L",
                       "LIN - Belpaire - Cammaerts" = "Belpaire | Cammaerts",
                       "LISEC - Neven & Beckers" = "Neven | Beckers",
                       "Lot Hebbelinck" = "Hebbelinck L",
                       "Luc Van Assche" = "Van Assche L",
                       "Marjolein" = "Messiaen M",
                       "NULL" = "",
                       "Paul van sanden" = "Van Sanden P",
                       "Pieter Cox" = "Cox P",
                       "Pieter Van Dorsselaer" = "Van Dorsselaer P",
                       "Rik Clicque" = "Clicque R",
                       "Roeland Croket" = "Croket R",
                       "Thomas Gyselinck" = "Gyselinck T",
                       "Tom Van den Neucker" = "Van den Neucker T",
                       "Verslycke Tim" = "Verslycke T",
                       "VMM" = "VMM",
                       "VMM - Joost" = "Mertens J",
                       "VMM - Joost, 2004_KreeftenBBICalc_Warmoes" = "",
                       "VMM - Wim Gabriels" = "Gabriels W",
                       "VMM - Wim Gabriels, 2004_KreeftenBBICalc_Warmoes" = "Gabriels W",
                       "VMM - Wim Gabriels, 2004_KreeftenBBICalc_Warmoes, VMM - Joost" = "Gabriels W",
                       "waarnemingen" = "waarnemingen.be",
                       "waarnemingen - Dirk Hennebel" = "Hennebel D",
                       "waarnemingen - Hans de Blauwe" = "de Blauwe H",
                       "waarnemingen - Hans De Blauwe" = "de Blauwe H",
                       "Waarnemingen - Kevin Lambeets" = "Lambeets K",
                       "waarnemingen - Tom Van den Neucker" = "Van den Neucker T",
                       "Warmoes Thierry" = "Warmoes T",
                       "Wouters" = "Wouters K",
                       "Wouters, 2002" = "Wouters K",
                       "Xavier Vermeersch" = "Vermeersch X",
                       "zeehavens" = "Boets P",
                       .default = "",
                       .missing = ""))

individualCount

organismQuantity

organismQuantityType

sex

lifeStage

reproductiveCondition

behavior

establishmentMeans

occurrenceStatus

preparations

disposition

associatedMedia

associatedReferences

associatedSequences

associatedTaxa

otherCatalogNumbers

occurrence %<>% mutate(otherCatalogNumbers = 
                         paste0("INBO:NBN:",raw_taxon_occurrence_key))

occurrenceRemarks

organismID

organismName

organismScope

associatedOccurrences

associatedOrganisms

previousIdentifications

organismRemarks

materialSampleID

eventID

parentEventID

fieldNumber

eventDate

Dates can be found both in raw_sample_vague_date_start and raw_sample_vague_date_end Both variables are imported in Rstudio as character vectors and need to be converted to an object of class “date”.

occurrence %<>% 
  mutate(Date_start = as.Date (raw_sample_vague_date_start,"%Y-%m-%d")) %<>% 
  mutate(Date_end = as.Date (raw_sample_vague_date_end,"%Y-%m-%d")) 

Date_start and Date_endare not always identical:

with (occurrence, identical(Date_start, Date_end))

## [1] FALSE

Thus: dates will be expressed as: yyy-mm-dd when Date_start = Date_end yyy-mm-dd / yy-mm-dd when Date_start != Date_end

creating new column Date_interval when Date_start != Date_end

occurrence %<>% mutate(Date_interval = paste (Date_start, Date_end, sep ="/"))  

As it is unsure if GBIF can handle /in EventDate: we always use Date_start for eventDate when Date_start != Date_end, we use Date_interval for verbatimEventDate OR when Date_start = Date_end, we define no value for verbatimEventDate

EventDate:

occurrence %<>% mutate(eventDate = Date_start)

verbatimEventDate:

occurrence %<>% mutate (verbatimEventDate =
                          case_when (
                            raw_sample_vague_date_start == raw_sample_vague_date_end ~ "",
                            raw_sample_vague_date_start != raw_sample_vague_date_end ~ Date_interval
                          ))

Remove the Date_start, Date_end and Date_interval (only intermediate steps):

occurrence %<>% select (- c(Date_start, Date_end, Date_interval))

eventTime

startDayOfYear

endDayOfYear

year

month

day

verbatimEventDate

habitat

samplingProtocol

sampleSizeValue

sampleSizeUnit

samplingEffort

fieldNotes

eventRemarks

locationID

higherGeographyID

higherGeography

continent

occurrence %<>% mutate(continent = "Europe")

waterBody

islandGroup

island

country

countryCode

occurrence %<>% mutate(countryCode = "BE")

stateProvince

county

municipality

occurrence %<>% mutate(municipality = raw_location_name_item_name)

locality

verbatimLocality

occurrence %<>% mutate(verbatimLocality = raw_survey_event_location_name)

minimumElevationInMeters

maximumElevationInMeters

verbatimElevation

minimumDepthInMeters

maximumDepthInMeters

verbatimDepth

minimumDistanceAboveSurfaceInMeters

maximumDistanceAboveSurfaceInMeters

locationAccordingTo

locationRemarks

decimalLatitude

occurrence %<>% 
  mutate (coordinate = str_replace (raw_sample_lat, ",", ".")) %>%  # Change "," to "."
  mutate (decimalLatitude = round (as.numeric(coordinate), 5)) %>%  # round to 5 decimals
  select (-coordinate)                                              # remove intermediary vector "coordinate"

decimalLongitude

occurrence %<>%
  mutate (coordinate = str_replace (raw_sample_long, ",", ".")) %<>%  # Change "," to "."
  mutate (decimalLongitude = round (as.numeric(coordinate), 5)) %<>%  # round to 5 decimals
  select (-coordinate)                                                # remove intermediary vector "coordinate"

geodeticDatum

occurrence %<>% mutate (geodeticDatum = "WGS84")

coordinateUncertaintyInMeters

occurrence %<>% mutate(coordinateUncertaintyInMeters = "30")

coordinatePrecision

pointRadiusSpatialFit

verbatimCoordinates

verbatimLatitude / verbatimLongitude / verbatimCoordinateSystem / verbatimSRS

These DwC terms were taken together as the easiest and clearest way to map them is to split occurrence in two separate dataframes: one dataframe with coordinatesystem = Belgium Lambert 72 and one with coordinatesystem = decimal degrees.

First, to obtain verbatimLongitude and verbatimLatitude information, we need to split raw_sample_spatial_ref into two columns (separator = “,”): longitude and latitude (intermediate columns, will be removed later) and to replace “,” by “.” in coordinates expressed as decimal degrees:

occurrence %<>% 
  separate( raw_sample_spatial_ref,
            into = c("longitude", "latitude"),
            sep = ",",
            remove = F) %<>%
  mutate (longitude = str_replace(longitude, ",", ".")) %<>%
  mutate (latitude = str_replace(latitude, ",", "."))

Create one dataframe for verbatimCoordinateSystem = Belgium Lambert 72 and one for verbatimCoordinateSystem = decimal degrees:

occurrence.BD72 <- filter (occurrence, raw_sample_spatial_ref_system == "BD72")
occurrence.LTLN <- filter (occurrence, raw_sample_spatial_ref_system == "LTLN")

Dwc mapping for verbatimLongitude / verbatimLatitude / verbatimCoordinateSystem / verbatimSRS:

occurrence.BD72 %<>% 
  mutate(verbatimLongitude = as.character (round (as.numeric (longitude, digits = 0 )))) %<>%  # round to 0 digits, convert from numeric to character for later union
  mutate(verbatimLatitude  = as.character (round (as.numeric (latitude, digits = 0 )))) %<>%   # round to 0 digits, convert from numeric to character for later union
  mutate(verbatimCoordinateSystem = "Belgium Lambert 72") %<>%
  mutate(verbatimSRS = "Belgian Datum 1972")

occurrence.LTLN %<>% 
  mutate(verbatimLongitude = longitude) %<>%
  mutate(verbatimLatitude  = latitude) %<>% 
  mutate(verbatimCoordinateSystem = "decimal degrees") %<>%
  mutate(verbatimSRS = "WGS84")

merge both subset to new occurrence data frame:

occurrence <- union(occurrence.BD72, occurrence.LTLN)

remove intermediary columns longitude and latitude:

occurrence %<>% select(-c(longitude, latitude))

footprintWKT

footprintSRS

footprintSpatialFit

georeferencedBy

georeferencedDate

georeferenceProtocol

georeferenceSources

georeferenceVerificationStatus

georeferenceRemarks

geologicalContextID

earliestEonOrLowestEonothem

latestEonOrHighestEonothem

earliestEraOrLowestErathem

latestEraOrHighestErathem

earliestPeriodOrLowestSystem

latestPeriodOrHighestSystem

earliestEpochOrLowestSeries

latestEpochOrHighestSeries

earliestAgeOrLowestStage

latestAgeOrHighestStage

lowestBiostratigraphicZone

highestBiostratigraphicZone

lithostratigraphicTerms

group

formation

member

bed

identificationID

identificationQualifier

typeStatus

identifiedBy

give all unique name/group/organization records in raw_survey_event_comment (base for recordedBy and identifiedBy)

occurrence %>% select (raw_survey_event_comment) %>%
  distinct(raw_survey_event_comment) %>%
  arrange (raw_survey_event_comment) %>%
  kable()

replace these records by a (list of) person(s), in the recommended best format for identifiedBy

occurrence %<>% mutate (
  identifiedBy = recode (raw_survey_event_comment,
                         "2004_KreeftenBBICalc_Warmoes" = "Warmoes T", 
                         "VMM, 2004_KreeftenBBICalc_Warmoes" = "",
                         "2004_niet_BBICacl - Warmoes" = "",
                         "Claudio Salvo" = "Salvo C",
                         "D'udekem D'Acoz" = "d'Udekem d'Acoz",
                         "databank VMM" = "Boets P",
                         "Dirk en Walda Hennebel" = "Hennebel D | Hennebel W",
                         "eigen data VMM" = "Boets P",
                         "extra stalen" = "Boets P",
                         "Frank de Block-Burij" = "de Block-Burij F",
                         "Geert Vanloot" = "Vanloot G",
                         "Gérard" = "Gérard",
                         "Gérard, 1986" = "Gérard",
                         "Gunter Flipkens" = "Flipkens G",
                         "Hans de Blauwe" = "de Blauwe H",
                         "Herwig Mees" = "Mees H",
                         "IRSNB-Karel Wouters, 2002" = "Wouters K",
                         "Johan Auwerx" = "Boets P",
                         "Joost Mertens" = "Mertens J",
                         "Kobe Janssen" = "Janssen K",
                         "koen" = "Lock K",
                         "Koen Maes" = "Maes K",
                         "Leloup L." = "Leloup L",
                         "LIN - Belpaire - Cammaerts" = "Belpaire | Cammaerts",
                         "LISEC - Neven & Beckers" = "Neven | Beckers",
                         "Lot Hebbelinck" = "Hebbelinck L",
                         "Luc Van Assche" = "Van Assche L",
                         "Marjolein" = "Messiaen M",
                         "NULL" = "",
                         "Paul van sanden" = "Van Sanden P",
                         "Pieter Cox" = "Cox P",
                         "Pieter Van Dorsselaer" = "Van Dorsselaer P",
                         "Rik Clicque" = "Clicque R",
                         "Roeland Croket" = "Croket R",
                         "Thomas Gyselinck" = "Gyselinck T",
                         "Tom Van den Neucker" = "Van den Neucker T",
                         "Verslycke Tim" = "Verslycke T",
                         "VMM" = "Boets P",
                         "VMM - Joost" = "Mertens J",
                         "VMM - Joost, 2004_KreeftenBBICalc_Warmoes" = "",
                         "VMM - Wim Gabriels" = "Gabriels W",
                         "VMM - Wim Gabriels, 2004_KreeftenBBICalc_Warmoes" = "Gabriels W",
                         "VMM - Wim Gabriels, 2004_KreeftenBBICalc_Warmoes, VMM - Joost" = "Gabriels W",
                         "waarnemingen" = "waarnemingen.be",
                         "waarnemingen - Dirk Hennebel" = "Hennebel D",
                         "waarnemingen - Hans de Blauwe" = "de Blauwe H",
                         "waarnemingen - Hans De Blauwe" = "de Blauwe H",
                         "Waarnemingen - Kevin Lambeets" = "Lambeets K",
                         "waarnemingen - Tom Van den Neucker" = "Van den Neucker T",
                         "Warmoes Thierry" = "Warmoes T",
                         "Wouters" = "Wouters K",
                         "Wouters, 2002" = "Wouters K",
                         "Xavier Vermeersch" = "Vermeersch X",
                         "zeehavens" = "Boets P",
                         .default = "",
                         .missing = ""))

dateIdentified

identificationReferences

identificationVerificationStatus

identificationRemarks

taxonID

scientificNameID

acceptedNameUsageID

parentNameUsageID

originalNameUsageID

nameAccordingToID

namePublishedInID

taxonConceptID

scientificName

Dreissena (Dreissena) polymorpha is the only scientific name with the subgenus mentioned in the name. This doesn’t add much information and is removed (see issue #9)

occurrence %<>% mutate (scientificName = 
                          case_when (
                            raw_nameserver_recommended_scientific_name == "Dreissena (Dreissena) polymorpha" ~ "Dreissena polymorpha",
                            raw_nameserver_recommended_scientific_name != "Dreissena (Dreissena) polymorpha" ~ raw_nameserver_recommended_scientific_name
                          ) )

acceptedNameUsage

parentNameUsage

originalNameUsage

nameAccordingTo

namePublishedIn

namePublishedInYear

higherClassification

kingdom

occurrence %<>% mutate (kingdom = "Animalia")

phylum

class

order

family

genus

subgenus

specificEpithet

infraspecificEpithet

taxonRank

raw_nameserver_recommended_name_rank contains two values: “Spp” and “SubSpp” –> This should be “Species” and “Subspecies”:

occurrence %<>% mutate (taxonRank = 
                          case_when (
                            raw_nameserver_recommended_name_rank == "Spp" ~ "species",
                            raw_nameserver_recommended_name_rank == "SubSpp" ~ "subspecies"
                          ) )

verbatimTaxonRank

scientificNameAuthorship

occurrence %<>% mutate (scientificNameAuthorship = raw_nameserver_recommended_name_authority)

vernacularName

nomenclaturalCode

occurrence %<>% mutate (nomenclaturalCode = "ICZN")

taxonomicStatus

nomenclaturalStatus

taxonRemarks