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Alignment with CHESS

The Colorado Headwaters Ecological Spectroscopy Study (CHESS) publishes field vegetation surveys, leaf area index measurements, soil characterisation, terrain derivatives, spectroscopy, and LiDAR on ESS-DIVE. The chess-data repository downloads those datasets and maps their column names to BERVO. This page records the terms BERVO added, or amended, so that the mapping resolves. It addresses issue #29.

Sources

Source Used for
Issue #29 and its correction comment The gap list. The correction withdraws most of the soil gaps in the original post; the tables below follow the corrected list.
chess-data, data/mapped/bervo-mapping-curated.tsv The vegetation survey mapping and its NO_MATCH rows

How the alignment is recorded

  • A CHESS column name is written into the term's Comment after CHESS:, exactly as the dataset spells it. CHESS headers are dataset-specific rather than a controlled vocabulary, so they are not stored as synonyms.
  • CHESS measures some quantities that EcoSIM computes, such as leaf area index and canopy height. BERVO keeps one term per quantity; whether a value was observed or modelled belongs to the dataset, not to the term. No observed versus modelled term pairs were added.
  • Where a CHESS variable already had a BERVO term under another name, the CHESS name was added as a synonym and the column names went into the comment.

CHESS variables mapped to new BERVO terms

Vegetation structure

CHESS columns BERVO term Parent Unit
Vegetation_Cover, Cover_Percent, FractionalCover Fractional vegetation cover (BERVO:0001883) Land surface variable 1
Stem diameter (BERVO:0001884) Plant trait variable cm, m
Stem_DBH, DBH_1_CM, DBH_2_CM, DBH_Avg_CM Stem diameter at breast height (BERVO:0001885) Stem diameter cm
Crown_Class, Canopy_Position Crown class (BERVO:0001886) Plant trait variable categorical
ba Stand basal area (BERVO:0001887) Ecology variable m2.har-1
density, abla_density, pien_density, pico_density Stem count per unit area (BERVO:0001888) Ecology variable har-1, m-2

Stem diameter is the general form and exists so that a diameter taken at a different height has a home. Stem count per unit area counts stems; Plant population (BERVO:0000725) counts individuals, and the two differ for multi-stemmed plants.

Leaf area index

CHESS columns BERVO term Parent Unit
Le_2200, Le_FV2200, Le_WN Effective leaf area index (BERVO:0001889) Canopy variable m2.m-2
Plant area index (BERVO:0001890) Canopy variable m2.m-2

Plant area index has no CHESS column. It is what an optical canopy analyser measures before the woody correction, and the corrected columns are derived from it, so it is here as the quantity the corrections start from.

The method-specific true LAI columns (L_2200, L_SCATCOR, L_WN, L_LANG, L_ELLIP, L_FV2200) all map to Canopy leaf area index (BERVO:0001879). They differ in retrieval method, not in the quantity. The clumping columns (CII, ACF_2200, ACF_SCATCOR) map to Apparent clumping factor (BERVO:8000562). The scattering correction factors (SCATCOR_*, CHI_SCATCOR, S_SCATCOR) are instrument correction terms and were not given BERVO terms.

Terrain

CHESS columns BERVO term Parent Unit
twi Topographic wetness index (BERVO:0001891) Land surface variable dimensionless
tpi Topographic position index (BERVO:0001892) Land surface variable m
curvature Land surface curvature (BERVO:0001893) Land surface variable m-1
heat_load Heat load index (BERVO:0001894) Land surface variable dimensionless
folded_aspect_205 Folded aspect (BERVO:0001895) Aspect deg

Climate

CHESS columns BERVO term Parent Unit
cwd Climatic water deficit (BERVO:0001896) Soil and water variable mm
mean annual precipitation Mean annual precipitation (BERVO:0001897) Climate force variable mm

Soil

CHESS columns BERVO term Parent Unit
infiltrations Soil infiltration rate (BERVO:0001898) Soil and water variable mm.h-1
microbial biomass carbon Soil microbial biomass carbon (BERVO:0001899) Microbial biomass chemical element mg{C}.kg-1
microbial biomass nitrogen Soil microbial biomass nitrogen (BERVO:0001900) Microbial biomass chemical element mg{N}.kg-1
nitrite_nitrogen Soil nitrite content (BERVO:0001901) Soil biogeochemistry variable mg.kg-1
manganese Soil manganese content (BERVO:0001902) Soil and water variable mg{Mn}.kg-1
zinc Soil zinc content (BERVO:0001903) Soil and water variable mg{Zn}.kg-1
lime buffer capacity Soil lime buffer capacity (BERVO:0001904) Soil biogeochemistry variable mg{CaCO3}.kg-1/{pH}

Soil infiltration rate is the capacity measured with an infiltrometer under an unlimited supply of water. Infiltration into soil (BERVO:0001821) is the flux that actually enters the soil under the rain or irrigation present, the quantity EcoSIM and ATS exchange. They share a dimension and not a meaning.

CHESS variables mapped to existing BERVO terms

CHESS columns BERVO term Change made
Elevation, Elevation_m, Topographical_Elevation Measurement of altitude (BERVO:0000683) elevation added as a related synonym; columns noted in the comment. Three altitude variables overlap (BERVO:0000670, BERVO:0000676, BERVO:0000683) and which one should own the word is not settled
aet Evapotranspiration (BERVO:0001809) actual evapotranspiration and AET added as related synonyms, since a potential evapotranspiration term may follow
swe, delta_swe Snow water equivalent (BERVO:0001873) none; added for ATS in #65
L_* (true LAI, any method) Canopy leaf area index (BERVO:0001879) none
CII, ACF_* Apparent clumping factor (BERVO:8000562) none
Terrain_Aspect Aspect (BERVO:0000685) none
Vegetation_Height, Stem_Height Pft canopy height (BERVO:0000695) none
mean annual temperature Mean annual temperature (BERVO:0001371) none
soil properties listed in the issue's correction comment as given there none

Not added

  • Taxonomy (Taxon_*, GBIF_Taxon_ID, Vegetation_Species). Outside BERVO's scope. The link from species to plant functional type is a workflow question, not a variable.
  • Tree condition (Crown_Remaining, Health_Status, Damage_Mode, Trunk_Wound, Leaves_Remaining, Cones_Present) and cover type (Cover_Type, Cover_Class_Name). Field survey classifications with no biogeochemical counterpart yet. They can be raised separately if a use appears.
  • Spectroscopy and LiDAR products (hyperspectral reflectance, canopy water content from spectra, shade fraction, canopy height model, DTM/DSM). Data products rather than variables; deferred.
  • non-microbial biomass, mean seasonal temperature, and average seasonal precipitation. Too ambiguous to define without the dataset's own definition of the season.
  • Administrative columns (dates, photo references, plot identifiers, notes). Not variables.