EMODnet data format | Emodnet Biology

EMODnet data format

Three format options are presented to you upon downloading data throught the EMODnet Biology toolbox or upon using the webservice. The Basic Occurrence Data donwload provides you with all data necessary to do temporal spacial analysis of the different taxa. The Full Occurrence Data download provides additiontal information which may help interpret the basic data. The Full Occurrence Data and Parameters download provides you also with all qantitative data and facts associated to the occurrence or the sample.

Basic Occurrence Data

The Basic Occurrence Data download provides you data for the following 8 essential terms:

Term Definition DarwinCore URI
datasetid An identifier that refers to the metadata record of the dataset in the EMODnet Biology Catalog. http://rs.tdwg.org/dwc/terms/datasetID
datecollected A date in full ISO format (YYYY-MM-DDTHH:MM:SS) generated by EMODnet Biology based on the data in the fields yearcollected, monthcollected, daycollected and timeofday. Unknown information is stored as the minimum value (e.g. YYYY-01-01T00:00:00 would be used if only the year is known)  
decimallongitude The geographic longitude (in decimal degrees, using WGS84 / EPSG:4326) of the geographic center of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. http://rs.tdwg.org/dwc/terms/decimalLongitude
decimallatitude The geographic latitude (in decimal degrees, using WGS84 / EPSG:4326) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. http://rs.tdwg.org/dwc/terms/decimalLatitude
coordinateuncertaintyinmeters The horizontal distance (in meters) from the given decimallatitude and decimallongitude describing the smallest circle containing the whole of the Location. The value is left empty if the uncertainty is unknown, cannot be estimated, or is not applicable (because there are no coordinates). Zero is not a valid value for this term. http://rs.tdwg.org/dwc/terms/coordinateUncertaintyInMeters
scientificname The full name of the lowest taxon level that the specimen(s) can be identified as a member of; includes genus, specific epithet, and subspecific epithet (zool.) or infraspecific rank abbreviation, and infraspecific epithet. http://rs.tdwg.org/dwc/terms/scientificName
aphiaid A link generated by EMODnet Biology based on the scientificnameid that references the scientificname in the World Register of Marine Species.  
scientificnameaccepted The scientific name of the currently valid or accepted taxon, generated by EMODnet Biology by referencing the scientificnameid in the the World Register of Marine Species.  

Full Occurrence Data

The Full Occurrence Data download provides you data for the following terms.

Term Definition DarwinCore URI
modified The most recent date-time on which the record was changed. http://purl.org/dc/terms/modified
datasetid An identifier that refers to the metadata record of the dataset in the EMODnet Biology Catalog. http://rs.tdwg.org/dwc/terms/datasetID
institutioncode The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record. http://rs.tdwg.org/dwc/terms/institutionCode
collectioncode The name, acronym, code, or initialis identifying the collection or data set from which the record was derived. http://rs.tdwg.org/dwc/terms/collectionCode
eventid An identifier for the set of information associated with an Event (something that occurs at a place and time). May be a global unique identifier or an identifier specific to the data set. http://rs.tdwg.org/dwc/terms/eventID
datecollected A date in full ISO format (YYYY-MM-DDTHH:MM:SS) generated by EMODnet Biology based on the data in the fields yearcollected, monthcollected, daycollected and timeofday. Unknown information is stored as the minimum value (e.g. YYYY-01-01T00:00:00 would be used if only the year is known).  
seasoncollected The season (winter, spring, summer, authum) generated by EMODnet Biology based on the data in the fields monthcollected and daycollected.  
yearcollected The year during which the sample or observation occurred.  
startyearcollected For samples or observations that were taken over a duration of time this term contains the start year of the collecting event. If the collection date is uncertain, this term can be used to store the minimum year for of the interval for which there is certainty.  
endyearcollected For samples or observations that were taken over a duration of time this term contains the end year of the collecting event. If the exact year is uncertain, this term can be used to store the maximum year for of the interval for which there is certainty.  
monthcollected The month of the year during which the sample or observation occurred.  
startmonthcollected For samples or observations that were taken over a duration of time this term gives the start month of the collecting event.  
endmonthcollected For samples or observations that were taken over a duration of time this term gives the end month of the collecting event.  
daycollected The day of the year during which the sample or observation occurred.  
startdaycollected For samples or observations that were taken over a duration of time this term gives the start day of the collecting event.  
enddaycollected For samples or observations that were taken over a duration of time this term gives the end day of the collecting event.  
timeofday The time of the day a specimen was collected expressed as decimal hours from midnight (e.g. 12.0 = mid day, 13.5 = 1:30pm).  
starttimeofday For samples or observations that were taken over a duration of time this gives the start time of the day of the collecting event expressed as decimal hours from midnight (e.g. 12.0 = mid day, 13.5 = 1:30pm).  
endtimeofday For samples/observations/record events that were taken over a duration of time this gives the end time of the day of the collecting event expressed as decimal hours from midnight (e.g. 12.0 = mid day, 13.5 = 1:30pm).  
timezone Indicates the time zone for the timeofday measurement. An empty value indicates local time.  
waterbody The name of the water body in which the sample or observation occurred. http://rs.tdwg.org/dwc/terms/waterBody
country The name of the country or major administrative unit in which the sample or observation occurred. http://rs.tdwg.org/dwc/terms/country
stateprovince The name of the next smaller administrative region than country (state, province, canton, department, region, etc.) in which the sample or observation occurred. http://rs.tdwg.org/dwc/terms/stateProvince
county The full, unabbreviated name of the next smaller administrative region than stateProvince (county, shire, department, etc.) in which the sample or observation occurred. http://rs.tdwg.org/dwc/terms/county
recordnumber An identifier given to the Occurrence at the time it was recorded. Often serves as a link between field notes and an Occurrence record, such as a specimen collector's number. http://rs.tdwg.org/dwc/terms/recordNumber
fieldnumber An identifier given to the event in the field. Often serves as a link between field notes and the Event. http://rs.tdwg.org/dwc/terms/fieldNumber
decimallongitude The geographic longitude (in decimal degrees, using WGS84 / EPSG:4326) of the geographic center of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. http://rs.tdwg.org/dwc/terms/decimalLongitude
startdecimallongitude For samples or observations that are better represented as line features rather than point features (e.g. extended trawls or transects) this term indicates the starting longitude location from which the specimen was collected.  
enddecimallongitude For samples or observations that are better represented as line features rather than point features (e.g. extended trawls or transects) this term indicates the end longitude location from which the specimen was collected.  
decimallatitude The geographic latitude (in decimal degrees, using WGS84 / EPSG:4326) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. http://rs.tdwg.org/dwc/terms/decimalLatitude
startdecimallatitude For samples or observations that are better represented as line features rather than point features (e.g. extended trawls or transects) this term indicates the starting latitude location from which the specimen was collected.  
enddecimallatitude For samples or observations that are better represented as line features rather than point features (e.g. extended trawls or transects) this term indicates the end latitude location from which the specimen was collected.  
coordinateuncertaintyinmeters The horizontal distance (in meters) from the given decimallatitude and decimallongitude describing the smallest circle containing the whole of the Location. The value is left empty if the uncertainty is unknown, cannot be estimated, or is not applicable (because there are no coordinates). Zero is not a valid value for this term. http://rs.tdwg.org/dwc/terms/coordinateUncertaintyInMeters
georeferenceprotocol A description or reference to the methods used to determine the spatial footprint, coordinates, and uncertainties. http://rs.tdwg.org/dwc/terms/georeferenceProtocol
minimumdepthinmeters The minimum distance in metres below the surface of the water at which the collection/record was made; all material collected was at least this deep. Positive below the surface, negative above (e.g. collecting above sea level in tidal areas). http://rs.tdwg.org/dwc/terms/minimumDepthInMeters
maximumdepthinmeters The maximum distance in metres below the surface of the water at which the collection/record was made; all material collected was at most this deep. Positive below the surface, negative above (e.g. collecting above sea level in tidal areas). http://rs.tdwg.org/dwc/terms/maximumDepthInMeters
occurrenceid An identifier for the Occurrence. In the absence of a persistent global unique identifier, one is constructed from a combination of identifiers in the record that will most closely make the occurrenceID globally unique. http://rs.tdwg.org/dwc/terms/occurrenceID
scientificname The full name of the lowest taxon level that the specimen(s) can be identified as a member of; includes genus, specific epithet, and subspecific epithet (zool.) or infraspecific rank abbreviation, and infraspecific epithet. http://rs.tdwg.org/dwc/terms/scientificName
scientificnameid The LSID (life science identifier) which references the scientificname in the World Register of Marine Species. http://rs.tdwg.org/dwc/terms/scientificNameID
aphiaid A link generated by EMODnet Biology based on the scientificnameid that references the scientificname in the World Register of Marine Species.  
taxonrank The taxonomic rank of the scientificName, generated by EMODnet Biology by referencing the scientificnameid in the the World Register of Marine Species. http://rs.tdwg.org/dwc/terms/taxonRank
scientificnameaccepted The scientific name of the currently valid or accepted taxon, generated by EMODnet Biology by referencing the scientificnameid in the the World Register of Marine Species.  
scientificnameauthorship The authorship information for the scientificName of the currently valid or accepted taxon, formatted according to the conventions of the applicable nomenclaturalCode. http://rs.tdwg.org/dwc/terms/scientificNameAuthorship
aphiaidaccepted A link generated by EMODnet Biology based on the scientificnameid that references the currently valid or accepted name for the taxon in the World Register of Marine Species (http://www.marinespecies.org/).  
kingdom The kingdom in which the scientificName of the currently valid or accepted taxon is classified, generated by EMODnet Biology by referencing the scientificnameid in the the World Register of Marine Species. http://rs.tdwg.org/dwc/terms/kingdom
phylum The phylum in which the scientificName of the currently valid or accepted taxon is classified, generated by EMODnet Biology by referencing the scientificnameid in the the World Register of Marine Species. http://rs.tdwg.org/dwc/terms/phylum
class The class in which the scientificName of the currently valid or accepted taxon is classified, generated by EMODnet Biology by referencing the scientificnameid in the the World Register of Marine Species. http://rs.tdwg.org/dwc/terms/class
order The order in which the scientificName of the currently valid or accepted taxon is classified, generated by EMODnet Biology by referencing the scientificnameid in the the World Register of Marine Species. http://rs.tdwg.org/dwc/terms/order
family The family in which the scientificName of the currently valid or accepted taxon is classified, generated by EMODnet Biology by referencing the scientificnameid in the the World Register of Marine Species. http://rs.tdwg.org/dwc/terms/family
genus The genus in which the scientificName of the currently valid or accepted taxon is classified, generated by EMODnet Biology by referencing the scientificnameid in the the World Register of Marine Species. http://rs.tdwg.org/dwc/terms/genus
subgenus The subgenus in which the scientificName of the currently valid or accepted taxon is classified, generated by EMODnet Biology by referencing the scientificnameid in the the World Register of Marine Species. http://rs.tdwg.org/dwc/terms/subgenus
specificepithet The first or species epithet (species name) of the scientificName of the currently valid or accepted taxon, generated by EMODnet Biology by referencing the scientificnameid in the the World Register of Marine Species. http://rs.tdwg.org/dwc/terms/specificEpithet
infraspecificepithet The lowest or terminal infraspecific epithet (subspecies name) of the scientificName of the currently valid or accepted taxon, generated by EMODnet Biology by referencing the scientificnameid in the the World Register of Marine Species. http://rs.tdwg.org/dwc/terms/infraspecificEpithet
occurrenceremarks Comments or notes about the Occurrence. http://rs.tdwg.org/dwc/terms/occurrenceRemarks
basisofrecord The specific nature of the data record. http://rs.tdwg.org/dwc/terms/basisOfRecord
typestatus Indicates the kind of nomenclatural type that a specimen represents, for example holotype, syntype, paratype, lectotype, paralectotype, neotype, schizotype, allotype, hapantotype. http://rs.tdwg.org/dwc/iri/typeStatus
catalognumber An identifier (preferably unique) for the record within the data set or collection. http://rs.tdwg.org/dwc/terms/catalogNumber
references Gives the web address of the page where more information on this particular record (not on the whole dataset) can be found. http://purl.org/dc/terms/references
recordedby A list (concatenated and separated) of names of people, groups, or organizations responsible for recording the original Occurrence. The primary collector or observer, especially one who applies a personal identifier (recordNumber), should be listed first. http://rs.tdwg.org/dwc/terms/recordedBy
identifiedby A list (concatenated and separated) of names of people, groups, or organizations who assigned the Taxon to the subject. http://rs.tdwg.org/dwc/terms/identifiedBy
yearidentified The year on which the subject was identified as representing the Taxon.  
monthidentified The month on which the subject was identified as representing the Taxon.  
dayidentified The day on which the subject was identified as representing the Taxon.  
preparations A preparation or preservation method for a specimen. http://rs.tdwg.org/dwc/iri/preparations
samplingeffort The amount of effort expended during an Event. http://rs.tdwg.org/dwc/terms/samplingEffort
samplingprotocol The method or protocol used during an Event. http://rs.tdwg.org/dwc/iri/samplingProtocol
qc

The QC flag generated by EMODnet Biology associated to the occurrence. The flag indicated the completenes and fit for purposeness of the record. Values are

  • 30: passes all checks
  • 26: the taxon rank is higher than genus level
  • 24: the taxon was not matched with the World Register of Marine Species
  • 22: the decimallatitude and/or decimallongitude have a 0 coordinate
  • 18: the taxon rank is higher than genus level and the decimallatitude and/or decimallongitude have a 0 coordinate
  • 16: the taxon was not matched with the World Register of Marine Species and the decimallatitude and/or decimallongitude have a 0 coordinate
  • 14: the decimallatitude and/or decimallongitude values are beyond the possible limits
  • 6: the decimallatitude and/or decimallongitude values are missing
  • 2: the taxon rank is higher than genus level and the decimallatitude and/or decimallongitude values are missing
 

Full Occurrence Data and Parameters

This will provide you with all terms from the Full Occurrence Data download (see above) and all parameters with data for the selected records. These parameters include both abiotic measurements (e.g. temperature, grainsize,... ), environmental facts (e.g. habitat), biotic measurements (e.g. abundance, lengths,... ), biotic descriptors (e.g. lifestage, sex,...) and metadata (e.g. sampling instrument, surface area, ... ). The data of these terms have been standardised: measurements have been recalculated to common unit while facts and descriptors have been standerdised using controlled vocabularies.

The data file is accompagnied by a file (params.csv) which contains definitions for all downloaded parameters aswell as the original units and the conversion factor used to standerdise these data. Next to each parameter a link to an IPT resource is provided where you can access the original data of the dataset where this parameter is included.

If the data sampling contains an hierarchical structure, then additional terms (cruise, stationVisit, sample, subsample, quadrat, transect) are added which contain an identifier that can be used to group all records that refer to a specific event.

 

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