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Genomic Biodiversity Interest Group
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DwC Mapping - MIXS:0000018 depth #13

Closed tucotuco closed 3 years ago

tucotuco commented 3 years ago
Field Value
subject_id http://rs.tdwg.org/dwc/terms/verbatimDepth
subject_definition The original description of the depth below the local surface.
subject_usage_notes
subject_examples 100-200 m
predicate_id skos:narrowMatch
object_id MIXS:0000018
object_label depth
object definition Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples
object source https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
comment In Darwin Core, according to best practices, depth is measured in water from an air-water surface, while in other media the corresponding terms are dwc:minimumDistanceAboveSurfaceInMeters and dwc:maximumDistanceAboveSurfaceInMeters, where the values would be negative for depth. Thus, for a sediment at the bottom of a lake, there would be an elevation of the lake surface, the depth of the top of the sediment in the lake, and minimum and maximum distances below the sediment surface within which a sample was taken.

or

Field Value
subject_id http://rs.tdwg.org/dwc/terms/minimumDistanceAboveSurfaceInMeters
subject_definition The lesser distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation.
subject_usage_notes
subject_examples -1.5 (below the surface). 4.2 (above the surface). For a 1.5 meter sediment core from the bottom of a lake (at depth 20m) at 300m elevation: verbatimElevation: 300m minimumElevationInMeters: 300, maximumElevationInMeters: 300, verbatimDepth: 20m, minimumDepthInMeters: 20, maximumDepthInMeters: 20, minimumDistanceAboveSurfaceInMeters: 0, maximumDistanceAboveSurfaceInMeters: -1.5.
predicate_id skos:narrowMatch
object_id MIXS:0000018
object_label depth
object definition Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples
object source https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
comment In Darwin Core, according to best practices, depth is measured in water from an air-water surface, while in other media the corresponding terms are dwc:minimumDistanceAboveSurfaceInMeters and dwc:maximumDistanceAboveSurfaceInMeters, where the values would be negative for depth. Thus, for a sediment at the bottom of a lake, there would be an elevation of the lake surface, the depth of the top of the sediment in the lake, and minimum and maximum distances below the sediment surface within which a sample was taken.

and

Field Value
subject_id http://rs.tdwg.org/dwc/terms/maximumDistanceAboveSurfaceInMeters
subject_definition The greater distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation.
subject_usage_notes
subject_examples -1.5 (below the surface). 4.2 (above the surface). For a 1.5 meter sediment core from the bottom of a lake (at depth 20m) at 300m elevation: verbatimElevation: 300m minimumElevationInMeters: 300, maximumElevationInMeters: 300, verbatimDepth: 20m, minimumDepthInMeters: 20, maximumDepthInMeters: 20, minimumDistanceAboveSurfaceInMeters: 0, maximumDistanceAboveSurfaceInMeters: -1.5.
predicate_id skos:narrowMatch
object_id MIXS:0000018
object_label depth
object definition Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples
object source https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
comment In Darwin Core, according to best practices, depth is measured in water from an air-water surface, while in other media the corresponding terms are dwc:minimumDistanceAboveSurfaceInMeters and dwc:maximumDistanceAboveSurfaceInMeters, where the values would be negative for depth. Thus, for a sediment at the bottom of a lake, there would be an elevation of the lake surface, the depth of the top of the sediment in the lake, and minimum and maximum distances below the sediment surface within which a sample was taken.
wardappeltans commented 3 years ago

In OBIS we use minimumDepthInMeters and maximumDepthInMeters. Positive values are below sea surface, negative values are above sea surface (e.g. intertidal zone).

raissameyer commented 3 years ago

In MIxS core V5, there is no true definition of depth. Currently, it only refers to the definitions in the respective environmental packages.

Please refer to the definitions of depth in the environmental packages

However, the definition of depth is the same for all environmental packages (given by @tucotuco above).

Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples

For the sediment and water packages there is an additional tot_depth_water_col to capture the sediment scenario @tucotuco gave in the SSSOM comment

Measurement of total depth of water column

ymgan commented 3 years ago

Related MIxS v6 issue: https://github.com/GenomicsStandardsConsortium/mixs/issues/63 Summary: depth is moved to MIxS core, definition is updated with true definition, no longer refers to somewhere else.

msweetlove commented 3 years ago

mapping MIxS:depth to DwC:minimumDistanceAboveSurfaceInMeters and DwC:maximumDistanceAboveSurfaceInMeters instead of DwC:verbatimDepth: vote +1

raissameyer commented 3 years ago

Additional mapping options for an exhaustive mapping:

Field Value
subject_id http://rs.tdwg.org/dwc/terms/minimumDepthInMeters
subject_definition The lesser depth of a range of depth below the local surface, in meters.
subject_value_syntax - expected_value - unit {float} - measurement value - meter
subject_examples 0, 100
predicate_id skos:narrowMatch
syntax_predicate_id skos:narrowMatch
object_id MIXS:0000018
object_label depth
object definition Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples
object_value_syntax - expected_value - unit {float} {unit} - measurement value - meter
object source https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
comment
syntax_comment The example offered by DwC does not include the unit "meter" as part of the entry in the field, whereas the MIxS syntax would expect the unit to be added.

and

Field Value
subject_id http://rs.tdwg.org/dwc/terms/maximumDepthInMeters
subject_definition The greater depth of a range of depth below the local surface, in meters.
subject_value_syntax - expected_value - unit {float} - measurement value - meter
subject_examples 0, 200
predicate_id skos:narrowMatch
syntax_predicate_id skos:narrowMatch
object_id MIXS:0000018
object_label depth
object definition Depth is defined as the vertical distance below local surface, e.g. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples
object_value_syntax - expected_value - unit {float} {unit} - measurement value - meter
object source https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
comment
syntax_comment The example offered by DwC does not include the unit "meter" as part of the entry in the field, whereas the MIxS syntax would expect the unit to be added.
raissameyer commented 3 years ago

Suggested syntax predicates for the mappings above https://github.com/tdwg/gbwg/issues/13#issue-805149090

Field Value
subject_id http://rs.tdwg.org/dwc/terms/verbatimDepth
subject_value_syntax - expected_value - unit verbatim
syntax_predicate_id skos:relatedMatch
object_id MIXS:0000018
object_value_syntax - expected_value - unit {float} {unit} - measurement value - meter
syntax_comment The DwC term expects a verbatim input (so anything really), while MIxS expects a {float} {unit} entry in meters

or

Field Value
subject_id http://rs.tdwg.org/dwc/terms/minimumDistanceAboveSurfaceInMeters
subject_value_syntax - expected_value - unit {float} - negative measurement value - meter
syntax_predicate_id skos:exactMatch
object_id MIXS:0000018
object_value_syntax - expected_value - unit {float} {unit} - measurement value - meter
syntax_comment The DwC term will expect a negative value here, while MIxS will not. Additionally, the example offered by DwC does not include the unit "meter" as part of the entry in the field, whereas the MIxS syntax would expect the unit to be added.

and

Field Value
subject_id http://rs.tdwg.org/dwc/terms/maximumDistanceAboveSurfaceInMeters
subject_value_syntax - expected_value - unit {float} - negative measurement value - meter
syntax_predicate_id skos:exactMatch
object_id MIXS:0000018
object_value_syntax - expected_value - unit {float} {unit} - measurement value - meter
syntax_comment The DwC term will expect a negative value here, while MIxS will not. Additionally, the example offered by DwC does not include the unit "meter" as part of the entry in the field, whereas the MIxS syntax would expect the unit to be added.
raissameyer commented 3 years ago

Based on the discussion in yesterday's meeting concerning how one term expecting negative values and the other term expecting positive values should effect the syntax predicate used, I've updated the syntax_predicate_id to skos:exactMatch for mapping http://rs.tdwg.org/dwc/terms/maximumDistanceAboveSurfaceInMeters and http://rs.tdwg.org/dwc/terms/minimumDistanceAboveSurfaceInMeters to MIxS:depth.

These are cases where the syntax is the same, but the range is different (which could be captured in the semantic predicate).