diff --git a/examples.md b/examples.md index 707adb7..bf4b676 100644 --- a/examples.md +++ b/examples.md @@ -2,19 +2,19 @@ **Contents** -- [Fish abundance & distribution](#fish-abundance--distribution) -- [Hard coral cover & composition](#hard-coral-cover--composition) -- [Invertebrates abundance & distribution](#invertebrates-abundance--distribution) -- [Macroalgae canopy cover & composition](#macroalgae-canopy-cover--composition) -- [Mangroves cover & composition](#mangroves-cover--composition) -- [Marine birds abundance & distribution](#marine-birds-abundance--distribution) -- [Marine mammals abundance & distribution](#marine-mammals-abundance--distribution) -- [Marine turtles abundance & distribution](#marine-turtles-abundance--distribution) - - [Survey & sighting data](#survey--sighting-data) -- [Microbes biomass & diversity](#microbes-biomass--diversity) -- [Phytoplankton biomass & diversity](#phytoplankton-biomass--diversity) -- [Seagrass cover & composition](#seagrass-cover--composition) -- [Zooplankton biomass & diversity](#zooplankton-biomass--diversity) +- [Fish abundance & distribution](#fish-abundance-and-distribution) +- [Hard coral cover & composition](#hard-coral-cover-and-composition) +- [Invertebrates abundance & distribution](#invertebrates-abundance-and-distribution) +- [Macroalgae canopy cover & composition](#macroalgae-canopy-cover-and-composition) +- [Mangroves cover & composition](#mangroves-cover-and-composition) +- [Marine birds abundance & distribution](#marine-birds-abundance-and-distribution) +- [Marine mammals abundance & distribution](#marine-mammals-abundance-and-distribution) +- [Marine turtles abundance & distribution](#marine-turtles-abundance-and-distribution) + - [Survey & sighting data](#survey-and-sighting-data) +- [Microbes biomass & diversity](#microbes-biomass-and-diversity) +- [Phytoplankton biomass & diversity](#phytoplankton-biomass-and-diversity) +- [Seagrass cover & composition](#seagrass-cover-and-composition) +- [Zooplankton biomass & diversity](#zooplankton-biomass-and-diversity) **Special data types:** @@ -25,22 +25,22 @@ - [Tracking data](other_data_types.html#tracking-data.html) - [Habitat](other_data_types.html#habitat-data) -#### Fish abundance & distribution +#### Fish abundance and distribution (example coming soon)

 

-#### Hard coral cover & composition +#### Hard coral cover and composition (example coming soon)

 

-#### Invertebrates abundance & distribution +#### Invertebrates abundance and distribution (example coming soon)

 

-#### Macroalgae canopy cover & composition +#### Macroalgae canopy cover and composition In this section we will encode a fictional macroalgal survey dataset into Darwin Core using the ENV-DATA approach, i.e. using an Event core with an Occurrence extension and an extendedMeasurementOrFact extension. @@ -93,12 +93,12 @@ And finally there is the MeasurementOrFact extension table, which has attributes | transect_2 | occ_5 | cover | [P01/current/SDBIOL10](http://vocab.nerc.ac.uk/collection/P01/current/SDBIOL10/) | 4 || percent | [P06/current/UPCT](http://vocab.nerc.ac.uk/collection/P06/current/UPCT) | | transect_2 | occ_6 | cover | [P01/current/SDBIOL10](http://vocab.nerc.ac.uk/collection/P01/current/SDBIOL10/) | 16 || percent | [P06/current/UPCT](http://vocab.nerc.ac.uk/collection/P06/current/UPCT) | -#### Mangroves cover & composition +#### Mangroves cover and composition (example coming soon)

 

-#### Marine birds abundance & distribution +#### Marine birds abundance and distribution The example for ENV-DATA collected with marine bird sightings/occurrences is based on the dataset ["RV Investigator Voyage IN2017_V02 Seabird Observations, Australia (2017)"](https://www.marine.csiro.au/ipt/resource?r=in2017_v02_wov). In this dataset, seabird sightings were recorded continuously during daylight hours during a voyage to recover and redeploy moorings at the SOTS site, southwest of Tasmania, Australia, in March 2017. Observations were made from c.30 minutes before sunrise to c.30 minutes after sunset, extending to 300m in the forward quadrant with the best viewing conditions. There were 1200 observations from 38 species of birds along with 3 cetacean species and one seal. This example will focus on the ENV-DATA associated with the bird sightings. The most frequently sighted bird species were *Puffinus tenuirostris* (Short-tailed Shearwater) and *Pachyptila turtur* (Fairy Prion). @@ -108,59 +108,29 @@ For this dataset, human observation recorded individual bird sightings (thus, ea The Occurrence core is populated with the occurrence records of seabirds sighted during the RV voyages. Occurrence details and scientific names are provided here. All birds were observed above sea level, all `minimumDepthInMeters` and `maximumDepthInMeters` values equal zero. -| occurrenceID | eventDate | institutionCode | collectionCode | -|------------------|---------------------|------------------------------------------------|----------------| -| in2017_v02_00998 | 2017-03-17 01:07:00 | Australasian Seabird Group, BirdLife Australia | in2017_v02_wov | -| in2017_v02_01380 | 2017-03-19 22:26:00 | Australasian Seabird Group, BirdLife Australia | in2017_v02_wov | -| in2017_v02_01012 | 2017-03-17 02:38:00 | Australasian Seabird Group, BirdLife Australia | in2017_v02_wov | - -| basisOfRecord | recordedBy | organismQuantity | organismQuantityType | occurrenceStatus | -|------------------|-------------|------------------|----------------------|------------------| -| HumanObservation | EJW+CRC+TAH | 2 | individuals | present | -| HumanObservation | EJW+CRC+TAH | 1 | individuals | present | -| HumanObservation | EJW+CRC+TAH | 1 | individuals | present | - -| decimalLatitude | decimalLongitude | coordinateUncertaintyInMeters | coordinatePrecision | footprintWKT | -|-----------------|------------------|-------------------------------|---------------------|-----------------------------| -| -43.40741 | 147.45576 | 200 | 0.0018 | POINT (147.45576 -43.40741) | -| -45.98644 | 142.1445 | 200 | 0.0018 | POINT (142.14450 -45.98644) | -| -43.40728 | 147.45549 | 200 | 0.0018 | POINT (147.45549 -43.40728) | - -| scientificNameID | scientificName | scientificNameAuthorship | vernacularName | -|-------------------------------------------|---------------------------------|--------------------------|---------------------| -| urn:lsid:marinespecies.org:taxname:343991 | Morus serrator | (Gray,1843) | Australasian Gannet | -| urn:lsid:marinespecies.org:taxname:212648 | Pachyptila turtur | (Kuhl,1820) | Fairy Prion | -| urn:lsid:marinespecies.org:taxname:707545 | Chroicocephalus novaehollandiae | Stephens,1826 | Silver Gull | +| occurrenceID | eventDate | institutionCode | collectionCode | basisOfRecord | recordedBy | organismQuantity | organismQuantityType | occurrenceStatus | decimalLatitude | decimalLongitude | coordinateUncertaintyInMeters | coordinatePrecision | footprintWKT | +|------------------|---------------------|-------------------|-----------|--------------|-----------|---------------|-------------------|--------------|-------------|--------------|-------------------|--------------|-------------------| +| in2017_v02_00998 | 2017-03-17 01:07:00 | Australasian Seabird Group, BirdLife Australia | in2017_v02_wov | HumanObservation | EJW+CRC+TAH | 2 | individuals | present | -43.40741 | 147.45576 | 200 | 0.0018 | POINT (147.45576 -43.40741) | urn:lsid:marinespecies.org:taxname:343991 | Morus serrator | (Gray,1843) | Australasian Gannet | +| in2017_v02_01380 | 2017-03-19 22:26:00 | Australasian Seabird Group, BirdLife Australia | in2017_v02_wov | HumanObservation | EJW+CRC+TAH | 1 | individuals | present | -45.98644 | 142.1445 | 200 | 0.0018 | POINT (142.14450 -45.98644) | urn:lsid:marinespecies.org:taxname:212648 | Pachyptila turtur | (Kuhl,1820) | Fairy Prion | +| in2017_v02_01012 | 2017-03-17 02:38:00 | Australasian Seabird Group, BirdLife Australia | in2017_v02_wov | HumanObservation | EJW+CRC+TAH | 1 | individuals | present | -43.40728 | 147.45549 | 200 | 0.0018 | POINT (147.45549 -43.40728) | urn:lsid:marinespecies.org:taxname:707545 | Chroicocephalus novaehollandiae | Stephens,1826 | Silver Gull | **extendedMeasurementOrFact (eMoF) extension:** As shown in previous examples, the MeasurementOrFact extension table contains abiotic measurements or facts corresponding to an occurrence / sighting. Individual sightings and abiotic measurements are linked with `occurrenceID`. In the example dataset, the ENV-DATA consist of measurements taken during the moorings deployment at the SOTS site, at the time of the marine bird sightings. In addition to NERC vocabulary terms, authors also referenced the Australian Ocean Data Network (AODN) Discovery Parameter Vocabulary for *Sea-floor depth (m)* and *Sea Surface Temperature* as `measurementType`. NERC equivalents to the AODN terms are added as additional MeasurementOrFact (MoF) records. -| occurrenceID | measurementID | measurementType | measurementTypeID | -|------------------|-----------------------------------|---------------------------------|----------------------------------------------------------------| -| in2017_v02_00998 | in2017_v02_00998-depth | Sea-floor depth (m) | | -| in2017_v02_00998 | in2017_v02_00998-depth | Sea-floor depth | | -| in2017_v02_00998 | in2017_v02_00998-air_pressure | Air Pressure (hPa) | | -| in2017_v02_00998 | in2017_v02_00998-air_temp | Atmospheric temperature (deg C) | | -| in2017_v02_00998 | in2017_v02_00998-wov_sea_state | Sea state | | -| in2017_v02_00998 | in2017_v02_00998-sea_surface_temp | Sea surface temperature | | -| in2017_v02_00998 | in2017_v02_00998-sea_surface_temp | Sea surface temperature | | -| in2017_v02_00998 | in2017_v02_00998-wind_direction | Wind direction (deg) | | -| in2017_v02_00998 | in2017_v02_00998-wind_speed | Wind Speed (knt) | | - -| measurementValue | measurementValueID | measurementUnit | measurementUnitID | -|-----------------------|---------------------------------------------------|---------------------------------|-----------------------------------------------------| -| 73.0313 | NA | Metres | | -| 73.0313 | NA | Metres | | -| 1024.91385 | NA | hPa | | -| 15.3 | NA | degrees Celsius | | -| moderate 1.25 - 2.5 m | | | | -| 17.32 | NA | degrees Celsius | | -| 17.32 | NA | degrees Celsius | | -| 283 | NA | degrees | | -| 5.49 | NA | Knots (nautical miles per hour) | | - -#### Marine mammals abundance & distribution +| occurrenceID | measurementID | measurementType | measurementTypeID | measurementValue | measurementValueID | measurementUnit | measurementUnitID | +|------------------|-----------------------------------|---------------------------------|----------------------------------------------------------------|--------------------|---------------------------------------------------|---------------------------------|-----------------------------------------------------| +| in2017_v02_00998 | in2017_v02_00998-depth | Sea-floor depth (m) | |73.0313 | NA | Metres | | +| in2017_v02_00998 | in2017_v02_00998-depth | Sea-floor depth | |73.0313 | NA | Metres | | +| in2017_v02_00998 | in2017_v02_00998-air_pressure | Air Pressure (hPa) | |1024.91385 | NA | hPa | | +| in2017_v02_00998 | in2017_v02_00998-air_temp | Atmospheric temperature (deg C) | |15.3 | NA | degrees Celsius | | +| in2017_v02_00998 | in2017_v02_00998-wov_sea_state | Sea state | | moderate 1.25 - 2.5 m | | | | +| in2017_v02_00998 | in2017_v02_00998-sea_surface_temp | Sea surface temperature | | 17.32 | NA | degrees Celsius | | +| in2017_v02_00998 | in2017_v02_00998-sea_surface_temp | Sea surface temperature | | 17.32 | NA | degrees Celsius | | +| in2017_v02_00998 | in2017_v02_00998-wind_direction | Wind direction (deg) | | 283 | NA | degrees | | +| in2017_v02_00998 | in2017_v02_00998-wind_speed | Wind Speed (knt) | | 5.49 | NA | Knots (nautical miles per hour) | | + +#### Marine mammals abundance and distribution In this section we will explore how to encode a survey data set into Darwin Core using the ENV-DATA approach. As an example, sections of the actual data set of [CETUS: Cetacean monitoring surveys in the Eastern North Atlantic](http://ipt.vliz.be/eurobis/resource?r=cetus_cetaceans), is used. @@ -174,9 +144,9 @@ Create the Event core table by extracting all events and populating attributes. | eventID | parentEventID | eventDate | footprintWKT | footprintSRS | |--------------------|---------------|-----------------|----------------------------------------------------------------------------------------------------------------|--------------| | Madeira | | 2012-07/2017-09 | POLYGON ((-16.74 31.49, -16.74 41.23, -8.70 41.23, -8.70 31.49, -16.74 31.49)) | EPSG:4326 | -| Madeira:Cruise-001 | Madeira | 2012-07 | MULTIPOINT ( (-8.7 41.19), (-9.15 38.7)) | EPSG:4326 | -| Madeira:Cruise-002 | Madeira | 2012-07 | MULTIPOINT ( (-9.15 38.7), (-16.73 32.74)) | EPSG:4326 | -| Madeira:Cruise-003 | Madeira | 2012-07 | MULTIPOINT ( (-16.73 32.74), (-9.15 38.7)) | EPSG:4326 | +| Madeira:Cruise-001 | Madeira | 2012-07 | MULTIPOINT ( (-8.7 41.19), (-9.15 38.7)) | EPSG:4326 | +| Madeira:Cruise-002 | Madeira | 2012-07 | MULTIPOINT ( (-9.15 38.7), (-16.73 32.74)) | EPSG:4326 | +| Madeira:Cruise-003 | Madeira | 2012-07 | MULTIPOINT ( (-16.73 32.74), (-9.15 38.7)) | EPSG:4326 | **Occurrence extension:** @@ -196,21 +166,21 @@ Construct the Occurrence extension table with the scientific names and links to And finally, the extendedMeasurementOrFact extension table has attributes of the zones (such as Vessel speed and Vessel Heading), the Transects (such as Wave height and Wind speed), and the Positions (such as Visibility and the Number of smaal/big ships >20m). Attributes of Positions point to the Occurrence extension table using the `occurrenceID` column (see `Transect-01:Pos-0001` and `Transect-01:Pos-0002` highlighted in blue and orange, respectively). -| id | occurrenceID | measurementType | measurementTypeID | measurementValue | measurementUnit | measurementUnitID | -|-----------------------------------------|-------------------|------------------------------|----------------------------------------------------------|------------------|---------------------------------|------------------------------------------------------| -| Madeira:Cruise-001 | | Vessel name | [Q01/current/Q0100001](http://vocab.nerc.ac.uk/collection/Q01/current/Q0100001/) | Monte da Guia | | | -| Madeira:Cruise-001:Transect-01 | | Length of the track | [P01/current/DSRNCV01](http://vocab.nerc.ac.uk/collection/P01/current/DSRNCV01/) | 39.75 | km | [P06/current/ULKM](http://vocab.nerc.ac.uk/collection/P06/current/ULKM/) | -| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Visibility | | 2000-4000 | Meters | [P06/current/ULAA](http://vocab.nerc.ac.uk/collection/P06/current/ULAA/) | -| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Wind speed | [P01/current/WMOCWFBF](http://vocab.nerc.ac.uk/collection/P01/current/WMOCWFBF/) | 1 | Beaufort scale | | -| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Wave height | | 2 | Douglas scale | | -| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Number of big ships (>20m) | | 3 | | | -| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Vessel heading | [P01/current/HDNGGP01](http://vocab.nerc.ac.uk/collection/P01/current/HDNGGP01/) | 206 | Degrees | [P06/current/UAAA](http://vocab.nerc.ac.uk/collection/P06/current/UAAA/) | -| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Number of small ships (<20m) | | 0 | | | -| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Vessel speed | [P01/current/APSAGP01](http://vocab.nerc.ac.uk/collection/P01/current/APSAGP01/) | 16 | Knots (nautical miles per hour) | [P06/current/UKNT](http://vocab.nerc.ac.uk/collection/P06/current/UKNT/) | +| id | occurrenceID | measurementType | measurementTypeID | measurementValue | measurementUnit | measurementUnitID | +|--------------|----------------|---------------|--------------------------------|------------------|-----------------------|---------------| +| Madeira:Cruise-001 | | Vessel name | [Q01/current/Q0100001](http://vocab.nerc.ac.uk/collection/Q01/current/Q0100001/) | Monte da Guia | | | +| Madeira:Cruise-001:Transect-01 | | Length of the track | [P01/current/DSRNCV01](http://vocab.nerc.ac.uk/collection/P01/current/DSRNCV01/) | 39.75 | km | [P06/current/ULKM](http://vocab.nerc.ac.uk/collection/P06/current/ULKM/) | +| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Visibility | | 2000-4000 | Meters | [P06/current/ULAA](http://vocab.nerc.ac.uk/collection/P06/current/ULAA/) | +| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Wind speed | [P01/current/WMOCWFBF](http://vocab.nerc.ac.uk/collection/P01/current/WMOCWFBF/) | 1 | Beaufort scale | | +| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Wave height | | 2 | Douglas scale | | +| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Number of big ships (>20m) | | 3 | | | +| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Vessel heading | [P01/current/HDNGGP01](http://vocab.nerc.ac.uk/collection/P01/current/HDNGGP01/) | 206 | Degrees | [P06/current/UAAA](http://vocab.nerc.ac.uk/collection/P06/current/UAAA/) | +| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Number of small ships (<20m) | | 0 | | | +| Madeira:Cruise-001:Transect-01:Pos-0001 | CIIMAR-CETUS-0001 | Vessel speed | [P01/current/APSAGP01](http://vocab.nerc.ac.uk/collection/P01/current/APSAGP01/) | 16 | Knots (nautical miles per hour) | [P06/current/UKNT](http://vocab.nerc.ac.uk/collection/P06/current/UKNT/) | -#### Marine turtles abundance & distribution +#### Marine turtles abundance and distribution -##### Survey & sighting data +##### Survey and sighting data This section deals with encoding survey and/ or sighting data of sea turtles into Darwin Core using the ENV-DATA approach. Extracts from the actual data set of [Presence of sea turtles collected through Fixed-Line-Transect monitoring across the Western Mediterranean Sea (Civitavecchia-Barcelona route) between 2013 and 2017](https://ipt.vliz.be/eurobis/resource?r=cc_flt_cbar_13-17#anchor-description), are used as an example. @@ -218,81 +188,38 @@ This section deals with encoding survey and/ or sighting data of sea turtles int The Event core is created by extracting all sighting events and populating the attributes at each event. The events at the different levels are linked together using `eventID` and `parentEventID`. In the example dataset, turtle sightings have been recorded since 2007, along a ferry route between Italy and Spain, as part of the monitoring project FLT Med Net (Fixed Line Transect Mediterranean monitoring Network). Turtle sighting locations can be given by populating the fields `footprintWKT` and `footprintSRS` with location information. Sightings were recorded at different dates, therefore `eventDate` is populated at the transect level. -| id | modified | datasetID | datasetName | -|-----------------------|---------------------|----------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| TURTLE_CBAR_0043 | 2021-05-05 07:59:08 | | Presence of sea turtles collected through Fixed-Line-Transect monitoring across the Western Mediterranean Sea | -| TURTLE_CBAR_0045 | 2021-05-05 07:59:08 | | Presence of sea turtles collected through Fixed-Line-Transect monitoring across the Western Mediterranean Sea | -| TURTLE_CBAR_0045_0001 | 2021-05-05 07:59:08 | | Presence of sea turtles collected through Fixed-Line-Transect monitoring across the Western Mediterranean Sea | -| TURTLE_CBAR_0045_0002 | 2021-05-05 07:59:08 | | Presence of sea turtles collected through Fixed-Line-Transect monitoring across the Western Mediterranean Sea | - -| eventID | parentEventID | eventDate | -|-----------------------|------------------|-----------------------------------------------------| -| TURTLE_CBAR_0043 | | 2013-04-03T05:30:00+02:00/2013-04-03T16:00:00+02:00 | -| TURTLE_CBAR_0045 | | 2013-04-18T05:22:00+02:00/2013-04-18T15:53:00+02:00 | -| TURTLE_CBAR_0045_0001 | TURTLE_CBAR_0045 | 2013-04-18T05:55:00+02:00 | -| TURTLE_CBAR_0045_0002 | TURTLE_CBAR_0045 | 2013-04-18T08:35:00+02:00 | - -| eventRemarks | minimumDepthInMeters | maximumDepthInMeters | decimalLatitude | decimalLongitude | -|--------------|----------------------|----------------------|-----------------|------------------| -| transect | 0 | 0 | 41.26179967 | 4.933265167 | -| transect | 0 | 0 | 41.30371367 | 4.936571167 | -| sample | 0 | 0 | 41.3228 | 7.4984 | -| sample | 0 | 0 | 41.322845 | 5.995345 | - -| geodeticDatum | coordinateUncertaintyInMeters | footprintWKT | footprintSRS | -|---------------|-------------------------------|----------------------------------------------------------------|--------------| -| EPSG:4326 | 222970.2874 | LINESTRING (7.602633333333 41.24378333333, 2.263897 41.279816) | EPSG:4326 | -| EPSG:4326 | 225420.0359 | LINESTRING (7.636983333333 41.32418333333, 2.236159 41.283244) | EPSG:4326 | -| EPSG:4326 | | POINT | EPSG:4326 | -| EPSG:4326 | | POINT | EPSG:4326 | +| id | modified | datasetID | datasetName | eventID | parentEventID | eventDate | eventRemarks | minimumDepthInMeters | maximumDepthInMeters | decimalLatitude | decimalLongitude | geodeticDatum | coordinateUncertaintyInMeters | footprintWKT | footprintSRS | +|-----------------------|---------------------|----------------------------------------|-------------------------------------|----------------------|------------------|------------------------------------|------------|----------------------|----------------------|-----------------|------------------|----------|-------------------------------|----------------------------------------------------------------|--------------| +| TURTLE_CBAR_0043 | 2021-05-05 07:59:08 | | Presence of sea turtles collected through Fixed-Line-Transect monitoring across the Western Mediterranean Sea | TURTLE_CBAR_0043 | | 2013-04-03T05:30:00+02:00/2013-04-03T16:00:00+02:00 | transect | 0 | 0 | 41.26179967 | 4.933265167 | EPSG:4326 | 222970.2874 | LINESTRING (7.602633333333 41.24378333333, 2.263897 41.279816) | EPSG:4326 | +| TURTLE_CBAR_0045 | 2021-05-05 07:59:08 | | Presence of sea turtles collected through Fixed-Line-Transect monitoring across the Western Mediterranean Sea | TURTLE_CBAR_0045 | | 2013-04-18T05:22:00+02:00/2013-04-18T15:53:00+02:00 | transect | 0 | 0 | 41.30371367 | 4.936571167 | EPSG:4326 | 225420.0359 | LINESTRING (7.636983333333 41.32418333333, 2.236159 41.283244) | EPSG:4326 | +| TURTLE_CBAR_0045_0001 | 2021-05-05 07:59:08 | | Presence of sea turtles collected through Fixed-Line-Transect monitoring across the Western Mediterranean Sea | TURTLE_CBAR_0045_0001 | TURTLE_CBAR_0045 | 2013-04-18T05:55:00+02:00 | sample | 0 | 0 | 41.3228 | 7.4984 | EPSG:4326 | | POINT | EPSG:4326 | +| TURTLE_CBAR_0045_0002 | 2021-05-05 07:59:08 | | Presence of sea turtles collected through Fixed-Line-Transect monitoring across the Western Mediterranean Sea | TURTLE_CBAR_0045_0002 | TURTLE_CBAR_0045 | 2013-04-18T08:35:00+02:00 | sample | 0 | 0 | 41.322845 | 5.995345 | EPSG:4326 | | POINT | EPSG:4326 | **Occurrence extension:** The Occurrence extension contain details regarding the sighted animals and include `scientificName` and the links to the World Register of Marine Species in `scientificNameID`. The `EventID` references the events as in the Event core. This table further provides information on the `basisOfRecord` and `occurrenceStatus`. -| EventID | occurrenceID | datasetID | collectionCode | basisOfRecord | -|-----------------------|----------------------|----------------------------------------|-------------------|------------------| -| TURTLE_CBAR_0043 | AdL_TURTLE_CBAR_0001 | | TURTLE_CBAR_13-17 | HumanObservation | -| TURTLE_CBAR_0045 | AdL_TURTLE_CBAR_0004 | | TURTLE_CBAR_13-17 | HumanObservation | -| TURTLE_CBAR_0045_0001 | AdL_TURTLE_CBAR_0005 | | TURTLE_CBAR_13-17 | HumanObservation | -| TURTLE_CBAR_0045_0002 | AdL_TURTLE_CBAR_0006 | | TURTLE_CBAR_13-17 | HumanObservation | - -| catalogNumber | recordedBy | occurrenceStatus | -|----------------------|----------------------------------------------------------------------------------|------------------| -| AdL_TURTLE_CBAR_0001 | Ilaria Campana \| Miriam Paraboschi \| Erica Ercoli \| Erica | absent | -| AdL_TURTLE_CBAR_0004 | Antonella Arcangeli \| Cristina Berardi \| Lucilla Giulietti \| Claudia Boccardi | absent | -| AdL_TURTLE_CBAR_0005 | Antonella Arcangeli \| Cristina Berardi \| Lucilla Giulietti \| Claudia Boccardi | present | -| AdL_TURTLE_CBAR_0006 | Antonella Arcangeli \| Cristina Berardi \| Lucilla Giulietti \| Claudia Boccardi | present | - -| scientificNameID | scientificName | kingdom | scientificNameAuthorship | -|-------------------------------------------|-----------------|----------|--------------------------| -| urn:lsid:marinespecies.org:taxname:136999 | Cheloniidae | Animalia | Oppel, 1811 | -| urn:lsid:marinespecies.org:taxname:136999 | Cheloniidae | Animalia | Oppel, 1811 | -| urn:lsid:marinespecies.org:taxname:137205 | Caretta caretta | Animalia | Linnaeus, 1758 | -| urn:lsid:marinespecies.org:taxname:137205 | Caretta caretta | Animalia | Linnaeus, 1758 | +| EventID | occurrenceID | datasetID | collectionCode | basisOfRecord | catalogNumber | recordedBy | occurrenceStatus | scientificNameID | scientificName | kingdom | scientificNameAuthorship | +|--------------|-----------------|--------------------|-------------|------------------|----------------|---------------------|------------------|------------------------------|-----------------|----------|-------------------| +| TURTLE_CBAR_0043 | AdL_TURTLE_CBAR_0001 | | TURTLE_CBAR_13-17 | HumanObservation | AdL_TURTLE_CBAR_0001 | Ilaria Campana \| Miriam Paraboschi \| Erica Ercoli \| Erica | absent | urn:lsid:marinespecies.org:taxname:136999 | Cheloniidae | Animalia | Oppel, 1811 | +| TURTLE_CBAR_0045 | AdL_TURTLE_CBAR_0004 | | TURTLE_CBAR_13-17 | HumanObservation | AdL_TURTLE_CBAR_0004 | Antonella Arcangeli \| Cristina Berardi \| Lucilla Giulietti \| Claudia Boccardi | absent | urn:lsid:marinespecies.org:taxname:136999 | Cheloniidae | Animalia | Oppel, 1811 | +| TURTLE_CBAR_0045_0001 | AdL_TURTLE_CBAR_0005 | | TURTLE_CBAR_13-17 | HumanObservation | AdL_TURTLE_CBAR_0005 | Antonella Arcangeli \| Cristina Berardi \| Lucilla Giulietti \| Claudia Boccardi | present | urn:lsid:marinespecies.org:taxname:137205 | Caretta caretta | Animalia | Linnaeus, 1758 | +| TURTLE_CBAR_0045_0002 | AdL_TURTLE_CBAR_0006 | | TURTLE_CBAR_13-17 | HumanObservation | AdL_TURTLE_CBAR_0006 | Antonella Arcangeli \| Cristina Berardi \| Lucilla Giulietti \| Claudia Boccardi | present | urn:lsid:marinespecies.org:taxname:137205 | Caretta caretta | Animalia | Linnaeus, 1758 | **extendedMeasurementOrFact (eMoF) extension:** The extendedMeasurementOrFact extension (eMoF) for survey or sighting data contains additional attributes and measurements recorded during the survey, such as those regarding the Research Vessel, environmental conditions, and/ or animal measurements. These attributes are linked to the Occurrence extension using the `occurrenceID`. The example dataset contain measurements regarding the sampling method; speed and height of the Research Vessel as platform; wind force; sighting distance; as well as the count and developmental stage of the biological entity. -| id | occurrenceID | measurementType | measurementTypeID | -|-----------------------|----------------------|--------------------------------------------------------------------------------------------------------|----------------------------------------------------------| -| TURTLE_CBAR_0045 | AdL_TURTLE_CBAR_0004 | BEAUFORT WIND FORCE | | -| TURTLE_CBAR_0045 | AdL_TURTLE_CBAR_0004 | Platform height | | -| TURTLE_CBAR_0045 | AdL_TURTLE_CBAR_0004 | Sampling method | | -| TURTLE_CBAR_0045 | AdL_TURTLE_CBAR_0004 | Speed of measurement platform relative to ground surface {speed over ground} by unspecified GPS system | | -| TURTLE_CBAR_0045_0001 | AdL_TURTLE_CBAR_0005 | Development stage of biological entity specified elsewhere | | -| TURTLE_CBAR_0045_0001 | AdL_TURTLE_CBAR_0005 | Count (in assayed sample) of biological entity specified elsewhere | | -| TURTLE_CBAR_0045_0001 | AdL_TURTLE_CBAR_0005 | Sighting distance | | - -| measurementValue | measurementUnit | measurementUnitID | -|---------------------------------|---------------------------------|------------------------------------------------------| -| 0 | Beaufort scale | | -| 29 | Metres | | -| visual observation from ferries | | | -| 23.291 | Knots (nautical miles per hour) | | -| 1 | | | -| 20 | Metres | | +| id | occurrenceID | measurementType | measurementTypeID | measurementValue | measurementUnit | measurementUnitID | +|-----------------------|----------------------|--------------------------------------------------|---------------------------------------|-----------------------------|---------------------------------|--------------------------| +| TURTLE_CBAR_0045 | AdL_TURTLE_CBAR_0004 | BEAUFORT WIND FORCE | | 0 | Beaufort scale | | +| TURTLE_CBAR_0045 | AdL_TURTLE_CBAR_0004 | Platform height | | 29 | Metres | | +| TURTLE_CBAR_0045 | AdL_TURTLE_CBAR_0004 | Sampling method | | visual observation from ferries | | | +| TURTLE_CBAR_0045 | AdL_TURTLE_CBAR_0004 | Speed of measurement platform relative to ground surface {speed over ground} by unspecified GPS system | | 23.291 | Knots (nautical miles per hour) | | +| TURTLE_CBAR_0045_0001 | AdL_TURTLE_CBAR_0005 | Development stage of biological entity specified elsewhere | | | | | +| TURTLE_CBAR_0045_0001 | AdL_TURTLE_CBAR_0005 | Count (in assayed sample) of biological entity specified elsewhere | | 20 | Metres | | +| TURTLE_CBAR_0045_0001 | AdL_TURTLE_CBAR_0005 | Sighting distance | | | | + In addition to the measurements recorded by the example dataset, other measurements are also possible depending on the scope and aims of the survey project. The example dataset [Incidental sea snake and turtle bycatch records from the RV Southern Surveyor voyage SS199510, Gulf of Carpentaria, Australia (Nov 1995)](https://www.marine.csiro.au/ipt/resource?r=csiro_ss199510_reptile) for example, contain information regarding the length and weight of the biological entity as follows: @@ -300,110 +227,61 @@ In addition to the measurements recorded by the example dataset, other measureme | id | measurementID | occurrenceID | measurementType | measurementTypeID | measurementValue | measurementUnit | measurementUnitID | |--------------|---------------------|--------------|-----------------|---------------------------------------------------------|------------------|-----------------|-----------------------------------------------------| -| SS199510-001 | SS199510-001-length | SS199510-001 | Length | | 1250 | Millimetres | | -| SS199510-001 | SS199510-001-weight | SS199510-001 | Weight | | 800 | Grams | | -| SS199510-002 | SS199510-002-length | SS199510-002 | Length | | 1630 | Millimetres | | -| SS199510-002 | SS199510-002-weight | SS199510-002 | Weight | | 1477.7 | Grams | | +| SS199510-001 | SS199510-001-length | SS199510-001 | Length | | 1250 | Millimetres | | +| SS199510-001 | SS199510-001-weight | SS199510-001 | Weight | | 800 | Grams | | +| SS199510-002 | SS199510-002-length | SS199510-002 | Length | | 1630 | Millimetres | | +| SS199510-002 | SS199510-002-weight | SS199510-002 | Weight | | 1477.7 | Grams | | -#### Microbes biomass & diversity +#### Microbes biomass and diversity (example coming soon)

 

-#### Phytoplankton biomass & diversity +#### Phytoplankton biomass and diversity -This example deals with encoding phytoplankton observation data, including environmental data, into Darwin Core. Extracts from the actual data set [LifeWatch observatory data: phytoplankton observations by imaging flow cytometry (FlowCam) in the Belgian Part of the North Sea](https://obis.org/dataset/956d618f-91dc-4930-a253-cdf80ddb9371), are used as an example. +This example deals with encoding phytoplankton observation data, including environmental data, into Darwin Core. Extracts from the actual data set [LifeWatch observatory data: phytoplankton observations by imaging flow cytometry (FlowCam) in the Belgian Part of the North Sea](https://obis.org/dataset/956d618f-91dc-4930-a253-cdf80ddb9371), are used as an example. Phytoplankton data should adhere to guidelines by Martin-Cabrera et al., 2022: [Best practices and recommendations for plankton imaging data management: Ensuring effective data flow towards European data infrastructures. Version 1.](http://dx.doi.org/10.25607/OBP-1742). Specific guidelines for the Occurrence and eMoF tables are documented in this publication, and we emphasize important fields in this example. **Event core:** The Event core contains events at the different levels and are linked together with `eventID` and `parentEventID`. In this example,the dataset contains records pointing to the origin, the in-situ sampling position as well as a record referring to the ex-situ collection of living specimens. In this case, the the event type information is provided in `type`. The recommended practice for providing the countryCode is to use an ISO 3166-1-alpha-2 country code. If additional information regarding licencing is provided, these can be populated under `rightsHolder` and `accessRights`. The remaining Event core fields provide location data including `datasetID` and `datasetName`, `locationID`, `waterBody`, `maximumDepthInMeters`, `minimumDepthInMeters`, `decimalLongitude`, `decimalLatitude`, `coordinateUncertaintyInMeters`, `geodeticDatum` and `footprintSRS`. -| eventID | parentEventID | eventRemarks | eventDate | modified | -|-------------------------------------------------------|------------------------------|--------------|-----------------------------------------------------|---------------------| -| TripNR3242 | | cruise | 2017-05T13:18:00+00:00/2017-05T22:14:00+00:00 | 2021-10-21 15:52:00 | -| TripNR3242TripStationNR16781 | TripNR3242 | stationVisit | 2017-05-08T20:44:00+00:00/2017-05-08T20:55:00+00:00 | 2021-10-21 15:52:00 | -| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781 | sample | 2017-05-08T20:50:00+00:00 | 2021-10-21 15:52:00 | -| TripNR3242TripStationNR16781MidasTripActionID105598UW | TripNR3242TripStationNR16781 | sample | 2017-05-08T20:50:00+00:00 | 2021-10-21 15:52:00 | - -| datasetID | datasetName | locationID | waterBody | country | countryCode | -|----------------------------------------|-----------------------------------------------------------|------------|-----------|---------|-------------| -| | LifeWatch observatory data: phytoplankton observations... | | North Sea | Belgium | BE | -| | | JN17_5 | | | | -| | | JN17_5 | | | | -| | | JN17_5 | | | | - -| minimumDepthInMeters | maximumDepthInMeters | decimalLatitude | decimalLongitude | geodeticDatum | coordinateUncertaintyInMeters | footprintSRS | -|----------------------|----------------------|-----------------|------------------|---------------|-------------------------------|--------------| -| | | | | EPSG:4326 | | EPSG:4326 | -| 0 | 30.22 | 51.0131 | 1.90562 | EPSG:4326 | 1.11 | EPSG:4326 | -| 0 | 1 | 51.01203 | 1.90217 | EPSG:4326 | 1.11 | EPSG:4326 | -| 3 | 3 | 51.01203 | 1.90217 | EPSG:4326 | 1.11 | EPSG:4326 | +| eventID | parentEventID | eventRemarks | eventDate | modified | datasetID | datasetName | locationID | waterBody | country | countryCode | minimumDepthInMeters | maximumDepthInMeters | decimalLatitude | decimalLongitude | geodeticDatum | coordinateUncertaintyInMeters | footprintSRS | +|----------------------------|---------------------|--------------|----------------------------|---------------------|---------------------------|--------------------------------------|------------|-----------|---------|-------------|---------------------|----------------------|-----------------|------------------|---------------|-------------------------------|--------------| +| TripNR3242 | | cruise | 2017-05T13:18:00+00:00/2017-05T22:14:00+00:00 | 2021-10-21 15:52:00 | | LifeWatch observatory data: phytoplankton observations... | | North Sea | Belgium | BE | | | | | EPSG:4326 | | EPSG:4326 | +| TripNR3242TripStationNR16781 | TripNR3242 | stationVisit | 2017-05-08T20:44:00+00:00/2017-05-08T20:55:00+00:00 | 2021-10-21 15:52:00 | | | JN17_5 | | | | 0 | 30.22 | 51.0131 | 1.90562 | EPSG:4326 | 1.11 | EPSG:4326 | +| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781 | sample | 2017-05-08T20:50:00+00:00 | 2021-10-21 15:52:00 | | | JN17_5 | | | | 0 | 1 | 51.01203 | 1.90217 | EPSG:4326 | 1.11 | EPSG:4326 | +| TripNR3242TripStationNR16781MidasTripActionID105598UW | TripNR3242TripStationNR16781 | sample | 2017-05-08T20:50:00+00:00 | 2021-10-21 15:52:00 | | | JN17_5 | | | | 3 | 3 | 51.01203 | 1.90217 | EPSG:4326 | 1.11 | EPSG:4326 | **Occurrence extension:** -The Occurrence extension contains data of each occurrence with an `occurrenceID` and is linked to the Event core with the `eventID`. The Occurrence extension should provide information on the `basisOfRecord` and `occurrenceStatus`. Scientific names and links to the World Register of Marine Species should be provided under `scientificName` and `scientificNameID`, respectively. - -| eventID | occurrenceID | -|-----------------------------------------------------|---------------------------------------------------------------------------------------------------| -| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_(Pseudo-)pediastrum_5 | -| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_Actinoptychus senarius_5 | -| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_Actinoptychus splendens_5 | -| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_Actinoptychus_5 | +The Occurrence extension contains data of each occurrence with an `occurrenceID` and is linked to the Event core with the `eventID`. The Occurrence extension should provide information on the `basisOfRecord` and `occurrenceStatus`. Scientific names and links to the World Register of Marine Species should be provided under `scientificName` and `scientificNameID`, respectively. Recommended best practice is to always use the term of `MachineObservation` for imaging datasets derived from imaging instruments like this example, Additionally, the fields `identifiedBy` and `identificationVerificationStatus` are crucial to indicate whether the data has been validated, and by whom. While not shown in this example, `identificationReferences` and `associatedMedia` are also recommended to document the citation or algorithm software used in identification, and the persistent URL of annotated images, respectively. We know this dataset was validated because of information provided in the abstract and the eMoF table below, "identified and counted by image analysis and normalised to a unit volume of water body, validated by human". -| modified | basisOfRecord | occurrenceStatus | scientificNameID | scientificName | -|-----------|----------------|------------------|-------------------------------------------|-------------------------| -|2021-10-21 | Occurrence | absent | urn:lsid:marinespecies.org:taxname:160560 | Hydrodictyaceae | -|2021-10-21 | Occurrence | present | urn:lsid:marinespecies.org:taxname:148948 | Actinoptychus senarius | -|2021-10-21 | Occurrence | present | urn:lsid:marinespecies.org:taxname:148949 | Actinoptychus splendens | -|2021-10-21 | Occurrence | present | urn:lsid:marinespecies.org:taxname:148947 | Actinoptychus | +| eventID | occurrenceID | modified | basisOfRecord | occurrenceStatus | scientificNameID | scientificName | identifiedBy | identificationVerificationStatus | +|-----------------------------------------------------|------------------------------------------------------------|-----------|----------------|------------------|-------------------|-------------------------|--------------------|------| +| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_(Pseudo-)pediastrum_5 |2021-10-21 | MachineObservation | absent | urn:lsid:marinespecies.org:taxname:160560 | Hydrodictyaceae | Flanders Marine Institute | ValidatedByHuman | +| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_Actinoptychus senarius_5 | 2021-10-21 | MachineObservation | present | urn:lsid:marinespecies.org:taxname:148948 | Actinoptychus senarius | Flanders Marine Institute | ValidatedByHuman | +| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_Actinoptychus splendens_5 | 2021-10-21 | MachineObservation | present | urn:lsid:marinespecies.org:taxname:148949 | Actinoptychus splendens | Flanders Marine Institute | ValidatedByHuman | +| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_Actinoptychus_5 | 2021-10-21 | MachineObservation | present | urn:lsid:marinespecies.org:taxname:148947 | Actinoptychus | Flanders Marine Institute | ValidatedByHuman | **extendedMeasurementOrFact (eMoF) extension:** -The eMoF extension contains the environmental and measurement information and data of each occurrence. This extension is also linked to the Event core using the `eventID`, and linked to the Occurrence extension table using the `occurrenceID`. The various measurements are populated with `measurementID`, `measurementType`, `measurementTypeID`, `measurementUnit`, `measurementUnitID`, `measurementValue`, `measurementValueID`, `measurementAccuracy`, `measurementMethod`, `measurementDeterminedBy` and `measurementDeterminedDate`. In the example dataset,the LifeWatch observatory data was compiled using imaging flow cytometry (FlowCam) to observe and identify phytoplankton in the Belgian Part of the North Sea and recorded a number of measurements including abundance, lifestages, sampling device information as well as environmental measurements such as water temperature, salinity and conductivity with accompanying vocabulary. - -| id | occurrenceID | measurementType | -|-------------------------------------------------------|--------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------| -| TripNR3242 | | Platform Name | -| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_Actinoptychus_5 | Abundance of Actinoptychus (WoRMS:148947) per unit volume of the water body by image analysis | -| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_Actinoptychus senarius_5 | Abundance of Actinoptychus senarius (WoRMS:148948) per unit volume of the water body by image analysis | -| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_(Pseudo-)pediastrum_5 | Lifestage | -| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_Actinoptychus senarius_5 | Lifestage | -| TripNR3242TripStationNR16781MidasTripActionID105598 | | Sampling device aperture diameter | -| TripNR3242TripStationNR16781MidasTripActionID105598 | | Sampling instrument name | -| TripNR3242TripStationNR16781MidasTripActionID105598 | | Sampling net mesh size | -| TripNR3242TripStationNR16781MidasTripActionID105598UW | | Conductivity of the water body | -| TripNR3242TripStationNR16781MidasTripActionID105598UW | | Practical salinity of the water body | -| TripNR3242TripStationNR16781MidasTripActionID105598UW | | Temperature of the water body | - -| measurementTypeID | measurementValue | measurementValueID | measurementUnit | -|----------------------------------------------------------|---------------------|----------------------------------------------------------|--------------------| -| | Simon Stevin | | | -| | 2.24 | | specimens/L | -| | 1.12 | | specimens/L | -| | adult | | | -| | adult | | | -| | 0.4 | | meter | -| | Planktonnet Apstein | | | -| | 55 | | micrometer | -| | 3.916 | | Siemens per metre | -| | 34.295 | | Grams per kilogram | -| | 11.881 | | Degrees Celsius | - -| measurementUnitID | measurementDeterminedBy | measurementMethod | -|------------------------------------------------------|---------------------------|------------------------------------------------------------------------------------------------------------| -| | Flanders Marine Institute | | -| | Flanders Marine Institute | identified and counted by image analysis and normalised to a unit volume of water body, validated by human | -| | Flanders Marine Institute | identified and counted by image analysis and normalised to a unit volume of water body, validated by human | -| | Flanders Marine Institute | identified and counted by image analysis and normalised to a unit volume of water body, validated by human | -| | Flanders Marine Institute | identified and counted by image analysis and normalised to a unit volume of water body, validated by human | -| | Flanders Marine Institute | | -| | Flanders Marine Institute | | -| | Flanders Marine Institute | | -| | Flanders Marine Institute | Electrical conductivity of the water body by thermosalinograph, based on the UnderWaySystem of the ship | -| | Flanders Marine Institute | Practical salinity of the water body based on water from the UnderWaySystem of the ship | -| | Flanders Marine Institute | Temperature of the water body based on water from the UnderWaySystem of the ship | - -#### Seagrass cover & composition +The eMoF extension contains the environmental and measurement information and data of each occurrence. This extension is also linked to the Event core using the `eventID`, and linked to the Occurrence extension table using the `occurrenceID`. The various measurements are populated with `measurementID`, `measurementType`, `measurementTypeID`, `measurementUnit`, `measurementUnitID`, `measurementValue`, `measurementValueID`, `measurementAccuracy`, `measurementMethod`, `measurementDeterminedBy` and `measurementDeterminedDate`. In the example dataset, the LifeWatch observatory data was compiled using imaging flow cytometry (FlowCam) to observe and identify phytoplankton in the Belgian Part of the North Sea and recorded a number of measurements including abundance, lifestages, sampling device information as well as environmental measurements such as water temperature, salinity and conductivity with accompanying vocabulary. + +| id | occurrenceID | measurementType | measurementTypeID | measurementValue | measurementValueID | measurementUnit | measurementUnitID | measurementDeterminedBy | measurementMethod | +|---------------------|-------------------------------|-------------------------------|----------------|---------------------|----------------------------|--------------------|----------------|------------------------------|-------------------------| +| TripNR3242 | | Platform Name | | Simon Stevin | | | Flanders Marine Institute | | | +| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_Actinoptychus_5 | Abundance of Actinoptychus (WoRMS:148947) per unit volume of the water body by image analysis | | 2.24 | | specimens/L | | Flanders Marine Institute | identified and counted by image analysis and normalised to a unit volume of water body, validated by human | +| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_Actinoptychus senarius_5 | Abundance of Actinoptychus senarius (WoRMS:148948) per unit volume of the water body by image analysis | | 1.12 | | specimens/L | | Flanders Marine Institute | identified and counted by image analysis and normalised to a unit volume of water body, validated by human | +| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_(Pseudo-)pediastrum_5 | Lifestage | | adult | | | | Flanders Marine Institute | identified and counted by image analysis and normalised to a unit volume of water body, validated by human | +| TripNR3242TripStationNR16781MidasTripActionID105598 | TripNR3242TripStationNR16781MidasTripActionID105598occurenceIDTA_105598_Actinoptychus senarius_5 | Lifestage | | adult | | | +| TripNR3242TripStationNR16781MidasTripActionID105598 | | Sampling device aperture diameter | | 0.4 | | meter | | Flanders Marine Institute | +| TripNR3242TripStationNR16781MidasTripActionID105598 | | Sampling instrument name | | Planktonnet Apstein | | | | Flanders Marine Institute | +| TripNR3242TripStationNR16781MidasTripActionID105598 | | Sampling net mesh size | | 55 | | micrometer | | Flanders Marine Institute | | +| TripNR3242TripStationNR16781MidasTripActionID105598UW | | Conductivity of the water body | | 3.916 | | Siemens per metre | | Flanders Marine Institute | Electrical conductivity of the water body by thermosalinograph, based on the UnderWaySystem of the ship | +| TripNR3242TripStationNR16781MidasTripActionID105598UW | | Practical salinity of the water body | | 34.295 | | Grams per kilogram | | Flanders Marine Institute | Practical salinity of the water body based on water from the UnderWaySystem of the ship | +| TripNR3242TripStationNR16781MidasTripActionID105598UW | | Temperature of the water body | | 11.881 | | Degrees Celsius | | Flanders Marine Institute | Temperature of the water body based on water from the UnderWaySystem of the ship | + +#### Seagrass cover and composition The structure of the Event, Occurrence and extendedMeasurementOrFact extensions for Seagrass Cover & Composition is based on community feedback organised through the the Scientific Committee on Oceanic Research (SCOR): [Coordinated Global Research Assessment of Seagrass System (C-GRASS)](https://scor-int.org/group/158/). We acknowledge the work that the C-grass SCOR work group has done to develop a proposed scheme for completing Seagrass related extension files. @@ -413,19 +291,12 @@ Here encode seagrass survey data into Darwin Core according to the ENV-DATA appr The Event core table is created by extracting all events and attributes. All events are linked together using `eventID` and `parentEventID`. `eventDate` is populated at the transect level with the recommended format that conforms to ISO 8601-1:2019. `habitat` is populated as a category or description of the habitat in which the event occurred. Additional `fieldNotes` can also be provided if applicable. The recommended best practice for `countryCode` is to use an ISO 3166-1-alpha-2 country code. The remaining Event core fields comprise of location data including `maximumDepthInMeters`, `minimumDepthInMeters`, `decimalLongitude`, `decimalLatitude`, `coordinateUncertaintyInMeters`, `footprintWKT` and `footprintSRS`. Addtionally in the Event core, it is recommended to further include information regarding `license`, `rightsHolder`, `bibliographicCitation`, `institutionID`, `datasetID`, `institutionCode` and `datasetName`. -| eventID | parentEventID | eventDate | habitat | fieldNotes | countryCode | -|--------------------------------------------|--------------------------|------------|----------|------------|-------------| -| USBsg-chengue-pastocoral | | 2019-05-13 | seagrass | no notes | CO | -| USBsg-chengue-pastomanglar | | 2019-05-14 | seagrass | no notes | CO | -| USBsg-chengue-pastocoral-SquidPopTransect1 | USBsg-chengue-pastocoral | 2019-05-13 | seagrass | no notes | CO | -| USBsg-chengue-pastocoral-SquidPopTransect2 | USBsg-chengue-pastocoral | 2019-05-13 | seagrass | no notes | CO | - -| minimumDepthInMeters | maximumDepthInMeters | decimalLatitude | decimalLongitude | coordinateUncertaintyInMeters | footprintWKT | footprintSRS | -|----------------------|----------------------|-----------------|------------------|-------------------------------|-----------------------------------------------------------------------------------|--------------| -| 0.8 | 2 | 11.32021806 | -74.12753684 | 10 | POLYGON ((-74.1273259763024 11.320475512862,-74.1272978004008 11.3201655779439)) | EPSG:4326 | -| 0.8 | 0.8 | 11.31977189 | -74.12536879 | 10 | POLYGON ((-74.1253370891273 11.3195001294432,-74.1253337743154 11.3194968146313)) | EPSG:4326 | -| 0.8 | 2 | 11.32039927 | -74.12737404 | 50 | POINT (-74.1273740410759 11.3203992721869) | EPSG:4326 | -| 0.8 | 2 | 11.32027662 | -74.1273989 | 50 | POINT (-74.1273989021655 11.3202766241445) | EPSG:4326 | +| eventID | parentEventID | eventDate | habitat | fieldNotes | countryCode | minimumDepthInMeters | maximumDepthInMeters | decimalLatitude | decimalLongitude | coordinateUncertaintyInMeters | footprintWKT | footprintSRS | +|--------------------------------------------|--------------------------|------------|----------|------------|-------------|------------------|----------------------|-----------------|------------------|-------------------------------|-----------------------------------------------------------------------------------|--------------| +| USBsg-chengue-pastocoral | | 2019-05-13 | seagrass | no notes | CO | 0.8 | 2 | 11.32021806 | -74.12753684 | 10 | POLYGON ((-74.1273259763024 11.320475512862,-74.1272978004008 11.3201655779439)) | EPSG:4326 | +| USBsg-chengue-pastomanglar | | 2019-05-14 | seagrass | no notes | CO | 0.8 | 0.8 | 11.31977189 | -74.12536879 | 10 | POLYGON ((-74.1253370891273 11.3195001294432,-74.1253337743154 11.3194968146313)) | EPSG:4326 | +| USBsg-chengue-pastocoral-SquidPopTransect1 | USBsg-chengue-pastocoral | 2019-05-13 | seagrass | no notes | CO | 0.8 | 2 | 11.32039927 | -74.12737404 | 50 | POINT (-74.1273740410759 11.3203992721869) | EPSG:4326 | +| USBsg-chengue-pastocoral-SquidPopTransect2 | USBsg-chengue-pastocoral | 2019-05-13 | seagrass | no notes | CO | 0.8 | 2 | 11.32027662 | -74.1273989 | 50 | POINT (-74.1273989021655 11.3202766241445) | EPSG:4326 | **Occurrence extension:** @@ -472,80 +343,41 @@ The eMoF table contains the measurement information and data of each occurrence. | | 0.02725 | Grams per square metre | | | | 0 | Grams per square metre | | -#### Zooplankton biomass & diversity +#### Zooplankton biomass and diversity -Here we will encode zooplankton observation and environmental data into Darwin Core. Extracts from the actual dataset [LifeWatch observatory data: zooplankton observations by imaging (ZooScan) in the Belgian Part of the North Sea](https://obis.org/dataset/afa5b0e8-826d-4433-b698-beb176ef7880), are used as an example. +Here we will encode zooplankton observation and environmental data into Darwin Core. Extracts from the actual dataset [LifeWatch observatory data: zooplankton observations by imaging (ZooScan) in the Belgian Part of the North Sea](https://obis.org/dataset/afa5b0e8-826d-4433-b698-beb176ef7880), are used as an example. As with the phytoplankton example, zooplankton data should also adhere to guidelines by Martin-Cabrera et al., 2022: [Best practices and recommendations for plankton imaging data management: Ensuring effective data flow towards European data infrastructures. Version 1.](http://dx.doi.org/10.25607/OBP-1742). These Best Practices indicate that for imaging data like this example, the fields `identificationVerificationStatus` and `identifiedBy` are crucial to know whether the data has been validated, and by whom. `identificationReferences` is used to document the citation or algorithm software used in identification. When possible, `associatedMedia` should also be populated with the persistent URL of annotated images. **Event core:** The Event core contains events at the different levels and are linked together with `eventID` and `parentEventID`. In this example,the dataset contains records pointing to the origin, the in-situ sampling position as well as a record referring to the ex-situ collection of living specimens. In this case, the the event type information is provided in `type`. The recommended practice for providing the countryCode is to use an ISO 3166-1-alpha-2 country code. If additional information regarding licencing is provided, these can be populated under `rightsHolder` and `accessRights`. The remaining Event core fields provide location data including `datasetID` and `datasetName`, `locationID`, `waterBody`, `maximumDepthInMeters`, `minimumDepthInMeters`, `decimalLongitude`, `decimalLatitude`, `coordinateUncertaintyInMeters`, `geodeticDatum` and `footprintSRS`. -| eventID | parentEventID | eventRemarks | eventDate | modified | -|-----------------------------------------------------|-----------------------------|--------------|-----------------------------------------------------|---------------------| -| TripNR2547 | | cruise | 2013-07-22T06:58:00+00:00/2013-07-22T16:58:00+00:00 | 2021-06-23 14:54:00 | -| TripNR2547TripStationNR9781 | TripNR2547 | stationVisit | 2013-07-22T07:13:00+00:00/2013-07-22T07:26:00+00:00 | 2021-06-23 14:54:00 | -| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781 | sample | 2013-07-22T07:22:00+00:00 | 2021-06-23 14:54:00 | -| TripNR2547TripStationNR9781MidasTripActionID23024UW | TripNR2547TripStationNR9781 | sample | 2013-07-22T07:22:00+00:00 | 2021-06-23 14:54:00 | - -| datasetID | datasetName | locationID | waterBody | country | -|----------------------------------------|---------------------------------------------------------|------------|-------------------------------|---------| -| | LifeWatch observatory data: zooplankton observations... | | Belgian Part of the North Sea | Belgium | -| | LifeWatch observatory data: zooplankton observations... | 130 | | | -| | LifeWatch observatory data: zooplankton observations... | 130 | | | -| | LifeWatch observatory data: zooplankton observations... | 130 | | | - -| minimumDepthInMeters | maximumDepthInMeters | decimalLatitude | decimalLongitude | geodeticDatum | footprintSRS | -|----------------------|----------------------|-----------------|------------------|---------------|--------------| -| | | | | EPSG:4326 | EPSG:4326 | -| 0 | 13.4 | 51.27083333 | 2.905 | EPSG:4326 | EPSG:4326 | -| 0 | 0 | 51.2687318 | 2.901797 | EPSG:4326 | EPSG:4326 | -| 3 | 3 | 51.2687318 | 2.901797 | EPSG:4326 | EPSG:4326 | +| eventID | parentEventID | eventRemarks | eventDate | modified | datasetID | datasetName | locationID | waterBody | country | minimumDepthInMeters | maximumDepthInMeters | decimalLatitude | decimalLongitude | geodeticDatum | footprintSRS | +|--------------------|------------------|--------------|--------------------|---------------------|-----------------|------------------|------------|---------------------|---------|-----------|--------------|-----------------|-----------|---------------|--------| +| TripNR2547 | | cruise | 2013-07-22T06:58:00+00:00/2013-07-22T16:58:00+00:00 | 2021-06-23 14:54:00 | | LifeWatch observatory data: zooplankton observations... | | Belgian Part of the North Sea | Belgium | | | | | EPSG:4326 | EPSG:4326 | +| TripNR2547TripStationNR9781 | TripNR2547 | stationVisit | 2013-07-22T07:13:00+00:00/2013-07-22T07:26:00+00:00 | 2021-06-23 14:54:00 | | LifeWatch observatory data: zooplankton observations... | 130 | | | 0 | 13.4 | 51.27083333| 2.905 | EPSG:4326 | EPSG:4326 | +| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781 | sample | 2013-07-22T07:22:00+00:00 | 2021-06-23 14:54:00 | | LifeWatch observatory data: zooplankton observations... | 130 | | | 0 | 0 | 51.2687318 | 2.901797 | EPSG:4326 | EPSG:4326 | +| TripNR2547TripStationNR9781MidasTripActionID23024UW | TripNR2547TripStationNR9781 | sample | 2013-07-22T07:22:00+00:00 | 2021-06-23 14:54:00 | | LifeWatch observatory data: zooplankton observations... | 130 | | | 3 | 3 | 51.2687318 | 2.901797 | EPSG:4326 | EPSG:4326 | **Occurrence extension:** The Occurrence extension contains data of each occurrence with an `occurrenceID` and is linked to the Event core with the `eventID`. The Occurrence extension should provide information on the `basisOfRecord` and `occurrenceStatus`. Scientific names and links to the World Register of Marine Species should be provided under `scientificName` and `scientificNameID`, respectively. -| eventID | occurrenceID | -|---------------------------------------------------|---------------------------------------------------------------------------------------------| -| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781MidasTripActionID23024occurenceIDTA23024_Amphipoda_sub2_130 | -| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781MidasTripActionID23024occurenceIDTA23024_Annelida_sub2_130 | -| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781MidasTripActionID23024occurenceIDTA23024_Anomura_sub2_130 | -| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781MidasTripActionID23024occurenceIDTA23024_Appendicularia_sub2_130 | - -| modified | basisOfRecord | occurrenceStatus | scientificNameID | scientificName | -|------------|---------------|------------------|-------------------------------------------|----------------| -| 2021-06-22 | Occurrence | absent | urn:lsid:marinespecies.org:taxname:1135 | Amphipoda | -| 2021-06-22 | Occurrence | present | urn:lsid:marinespecies.org:taxname:882 | Annelida | -| 2021-06-22 | Occurrence | absent | urn:lsid:marinespecies.org:taxname:106671 | Anomura | -| 2021-06-22 | Occurrence | absent | urn:lsid:marinespecies.org:taxname:146421 | Appendicularia | +| eventID | occurrenceID | modified | basisOfRecord | occurrenceStatus | scientificNameID | scientificName | identifiedBy | identificationVerificationStatus | identificationReferences | +|-----------------------|--------------------|----------|---------------|------------------|--------------|-----------|-----------|-----------|-----------| +| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781MidasTripActionID23024occurenceIDTA23024_Amphipoda_sub2_130 | 2021-06-22 | Occurrence | absent | urn:lsid:marinespecies.org:taxname:1135 | Amphipoda | Jonas Mortelmans | ValidatedByHuman | RandomForest | +| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781MidasTripActionID23024occurenceIDTA23024_Annelida_sub2_130 | 2021-06-22 | Occurrence | present | urn:lsid:marinespecies.org:taxname:882 | Annelida | Jonas Mortelmans | ValidatedByHuman | RandomForest | +| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781MidasTripActionID23024occurenceIDTA23024_Anomura_sub2_130 | 2021-06-22 | Occurrence | absent | urn:lsid:marinespecies.org:taxname:106671 | Anomura | Jonas Mortelmans | ValidatedByHuman | RandomForest | +| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781MidasTripActionID23024occurenceIDTA23024_Appendicularia_sub2_130 | 2021-06-22 | Occurrence | absent | urn:lsid:marinespecies.org:taxname:146421 | Appendicularia | Jonas Mortelmans | ValidatedByHuman | RandomForest | **extendedMeasurementOrFact (eMoF) extension:** The eMoF extension table contains the measurement information and data of each occurrence. This extension is also linked to the Event core using the `eventID`, and linked to the Occurrence table using the `occurrenceID`. The various measurements are populated with `measurementType`, `measurementTypeID`, `measurementUnit`, `measurementUnitID`, `measurementValue`, `measurementValueID`, `measurementAccuracy`, `measurementMethod`, `measurementDeterminedBy` and `measurementDeterminedDate`. The example dataset of [LifeWatch observatory data: zooplankton observations by imaging (ZooScan) in the Belgian Part of the North Sea](https://obis.org/dataset/afa5b0e8-826d-4433-b698-beb176ef7880) recorded some ENV-DATA and organism measurements the can be used as an example of how to populate the respective fields, including conductivity of the water body; concentration of chlorophyll-a per unit volume of the water body; sampling instrument name; sampling net mesh size; lifestage of the organism observed; and abundance of the organism observed. -| id | occurrenceID | measurementType | -|-------------------------------------------------------|---------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------| -| TripNR3256TripStationNR17157MidasTripActionID106326 | | Sampling instrument name | -| TripNR3256TripStationNR17157MidasTripActionID106326 | | Sampling net mesh size | -| TripNR3529TripStationNR19242MidasTripActionID109631UW | | Conductivity of the water body | -| TripNR3529TripStationNR19243MidasTripActionID109634 | | Concentration of chlorophyll-a per unit volume of the water body | -| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781MidasTripActionID23024occurenceIDTA23024_Annelida_sub2_130 | Lifestage | -| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781MidasTripActionID23024occurenceIDTA23024_Annelida_sub2_130 | Abundance of Annelida (ITIS: 64357: WoRMS 882) per unit volume of the water body by image analysis | - -| measurementTypeID | measurementValue | measurementValueID | measurementUnit | -|----------------------------------------------------------|------------------|----------------------------------------------------------|----------------------| -| | Planktonnet WP2 | | | -| | 200 | | micrometer | -| | 4.05 | | Siemens per metre | -| | 1.42 | | Micrograms per litre | -| | unspecified | | | -| | 0.50 | | specimens/m³ | - -| measurementUnitID | measurementDeterminedBy | measurementMethod | -|------------------------------------------------------|---------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| | | | -| | | | -| | Flanders Marine Institute | Electrical conductivity of the water body by thermosalinograph, based on the UnderWaySystem of the ship | -| | Flanders Marine Institute | Concentration of chlorophyll-a per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | -| | Flanders Marine Institute | identified and counted by image analysis and normalised to a unit volume of water body, validated by human | -| | Flanders Marine Insitute | identified and counted by image analysis and normalised to a unit volume of water body, validated by human | +| id | occurrenceID | measurementType | measurementTypeID | measurementValue | measurementValueID | measurementUnit | measurementUnitID | measurementDeterminedBy | measurementMethod | +|---------------------------|------------------|--------------------|-----------------------|------------------|---------------------------------------|----------------------|-------------------------|---------------------------|------------------| +| TripNR3256TripStationNR17157MidasTripActionID106326 | | Sampling instrument name | | Planktonnet WP2 | | 200 | | micrometer | | | | +| TripNR3529TripStationNR19242MidasTripActionID109631UW| | Conductivity of the water body | | 4.05 | | Siemens per metre | | Flanders Marine Institute | Electrical conductivity of the water body by thermosalinograph, based on the UnderWaySystem of the ship | +| TripNR3529TripStationNR19243MidasTripActionID109634 | | Concentration of chlorophyll-a per unit volume of the water body | | 1.42 | | Micrograms per litre | | Flanders Marine Institute | Concentration of chlorophyll-a per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | +| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781MidasTripActionID23024occurenceIDTA23024_Annelida_sub2_130 | Lifestage | | unspecified | | | | Flanders Marine Institute | identified and counted by image analysis and normalised to a unit volume of water body, validated by human | +| TripNR2547TripStationNR9781MidasTripActionID23024 | TripNR2547TripStationNR9781MidasTripActionID23024occurenceIDTA23024_Annelida_sub2_130 | Abundance of Annelida (ITIS: 64357: WoRMS 882) per unit volume of the water body by image analysis | | 0.50 | | specimens/m³ | | Flanders Marine Insitute | identified and counted by image analysis and normalised to a unit volume of water body, validated by human |