depth checks

[ymgan]

obis-qc checks

Check	Fields	Flags	Absence	Dropped	Vandepitte et al. flag number
minimumDepthInMeters and maximumDepthInMeters should be present.	minimumDepthInMeters, maximumDepthInMeters	NO_DEPTH
minimumDepthInMeters and maximumDepthInMeters should be within range.	minimumDepthInMeters, maximumDepthInMeters	DEPTH_OUT_OF_RANGE
minimumDepthInMeters and maximumDepthInMeters should be less than or equal to the bathymetric depth.	minimumDepthInMeters, maximumDepthInMeters	DEPTH_EXCEEDS_BATH			19
minimumDepthInMeters exceeds maximumDepthInMeters	minimumDepthInMeters, maximumDepthInMeters	MIN_DEPTH_EXCEEDS_MAX			?

TDWG BDQ TG2 Tests

Validation

• *https://github.com/tdwg/bdq/issues/187
• *https://github.com/tdwg/bdq/issues/107
• https://github.com/tdwg/bdq/issues/24

*Parameterized

Amendment

• https://github.com/tdwg/bdq/issues/55

Parameters

test	default_parameters	obis-qc_current_parameters
VALIDATION_MAXDEPTH_INRANGE	bdq:minimumValidDepthInMeters default="0"	-100000
VALIDATION_MAXDEPTH_INRANGE	bdq:maximumValidDepthInMeters default="11000"	11000
VALIDATION_MINDEPTH_INRANGE	bdq:minimumValidDepthInMeters="0"	-100000
VALIDATION_MINDEPTH_INRANGE	bdq:maximumValidDepthInMeters="11000"	11000

GBIF flags

https://github.com/gbif/gbif-api/blob/dev/src/main/java/org/gbif/api/vocabulary/OccurrenceIssue.java

  /**
   * Set if supplied depth is not given in the metric system, for example using feet instead of
   * meters
   */
  DEPTH_NOT_METRIC(WARNING, DwcTerm.minimumDepthInMeters, DwcTerm.maximumDepthInMeters),

  /**
   * Set if depth is larger than 11,000m or negative.
   */
  DEPTH_UNLIKELY(WARNING, DwcTerm.minimumDepthInMeters, DwcTerm.maximumDepthInMeters),

  /**
   * Set if supplied minimum depth > maximum depth
   */
  DEPTH_MIN_MAX_SWAPPED(WARNING, DwcTerm.minimumDepthInMeters, DwcTerm.maximumDepthInMeters),

  /**
   * Set if depth is a non-numeric value
   */
  DEPTH_NON_NUMERIC(WARNING, DwcTerm.minimumDepthInMeters, DwcTerm.maximumDepthInMeters),

Visualization for OBIS data

Notebook here

enddepth <= 0

verbatimDepth, based on facet API

https://api.obis.org/v3/facet?facets=verbatimDepth

Related issues

• https://github.com/iobis/obis-qc/issues/14
• https://github.com/iobis/obis-issues/issues/182

[ymgan]

I think it is worth mentioning that depth should not be negative: https://github.com/tdwg/bdq/issues/107#issuecomment-961330986

Maybe we should take this into consideration while considering the parameters minimumValidDepthInMeters~

[albenson-usgs]

I think it also means adding support for minimumDistanceAboveSurface and maximumDistanceAboveSurface?

[ymgan]

I think it also means adding support for minimumDistanceAboveSurface and maximumDistanceAboveSurface?

@albenson-usgs I don't know. I am just mapping the obis-qc checks to checks in BDQ and GBIF. I leave the other tests relevant for the fields here since I had to go through them.

Unless OBIS indicates the capacity to implement the checks for minimumDistanceAboveSurface and maximumDistanceAboveSurface, I will not look at that (no funding haha) I am doing this outside office hours. Anyone else is welcome to look at that though.

[pieterprovoost]

@albenson-usgs Are there any existing BDQ checks that take into account minimumDistanceAboveSurface and maximumDistanceAboveSurface?

I do think we'll need to take these into account when deriving depth values, if I understand correctly a min/maximumDepthInMeters of 100 (which then becomes the reference surface) and a min/maximumDistanceAboveSurface of 10 should result in a derived depth value of 90 (for filtering purposes etc).

[ymgan]

Thanks @pieterprovoost! There isn't any test for minimumDistanceAboveSurfaceInMeters and maximumDistanceAboveSurfaceInMeters from BDQ. There are only tests for depth and elevations.

I don't see any test for min/maximumDistanceAboveSurfaceInMeters in GBIF either.

[ymgan]

2023-04-20 meeting

Determining min/maxValidDepthInMeters

• Question about intertidal transects, how to process samples where locations can be above/below the surface at different times was raised. Would you split it into different fields? (min/max depth, dist above surface) It seems to have been answered in this comment: https://github.com/tdwg/bdq/issues/107#issuecomment-961330986
• no clear consensus reached on whether minimum valid depth should be zero (to follow up on whether depth CAN be negative: https://github.com/tdwg/bdq/issues/107#issuecomment-1712515831)

Depth check against bathymetry

• Bathymetry layer with depth ranges by grid cell (min/max and not just a depth value) needed.
• EMODnet Bathymetry DTM has min max depth in addition to average, but only European waters
• % difference method is currently used (https://github.com/iobis/obis-qc/issues/14), but still results in many false positives especially when the terrain is very steep
• documentation should be improved: https://github.com/iobis/obis-issues/issues/182

Derived depth

• World ocean requires statistics with a single depth value, hence derived depth may be necessary when value is provided with multiple terms