Alignment with a survey of ESS-DIVE datasets
TROWEL extracted the variable names from 10 public ESS-DIVE datasets, drawn at random from those submitted between 2023-10-15 and 2026-10-15. This page records how each name is represented in BERVO, and the terms added for the ones it lacked (issue #171).
Source
| Source | Revision | Used for |
|---|---|---|
bioepic-data/trowel, data/essdive_random10_2026-10-15/ |
3b114b8 |
variable_names.tsv (189 names), data_dictionaries.tsv, and the dataset methods in results.tsv |
Seven of the ten datasets supplied names. Three keep their data in zip archives
or images and supplied none: the meteoric 10Be flux calibration, the
manganese-carbon model output, and the Utqiagvik phenology camera imagery. The
one name from the tundra land surface modelling archive,
196.19585 64.862976 1 1, is a data row read as a header.
The counts below are per dataset, so a name used by two datasets counts in
both. They sum to 192, or 193 with the tundra name. Four names appear in two
datasets each, treatment, depth, site, and date, which leaves the 189
unique names in variable_names.tsv.
| Dataset | Names | Topic |
|---|---|---|
| doi:10.15485/2395957 | 5 | Active layer and permafrost temperature, Teller 47, Alaska |
| doi:10.15485/3412618 | 22 | XANES, NEXAFS, and SANS of mineral-coated sands, Walker Branch, Tennessee |
| doi:10.15485/3015733 | 111 | Flooded coastal forest soil mesocosms: gas fluxes, porewater chemistry, CDOM, FTIR |
| doi:10.15485/2475392 | 14 | Leaf mass per area and leaf carbon and nitrogen, Seward Peninsula, Alaska |
| doi:10.15485/2998439 | 21 | Porewater chemistry in a brackish tidal marsh, Plum Island, Massachusetts |
| doi:10.15485/3020155 | 19 | Fungal mat growth and litter colonization, TRACE warming experiment, Puerto Rico |
Reducing names to variables
Most of the 189 names are not distinct variables. They reduce to about 45, by these rules:
- Summary and treatment suffixes are dropped. The mesocosm dataset reports
each porewater analyte as a mean and a standard deviation for each of three
treatments:
c(control),fw(freshwater flood), andbw(brackish water flood).sulfate fw mean,sulfate bw std, and the other five combinations are all Dissolved sulfate concentration. - Per-sample columns are not variables.
day 28 rep 2,quartz rep 1,fe oxide-coated sand rep 1,c before,fw after, and similar names head the columns of a spectrum, one per sample. In the same way,c1tobw2in the moisture file are one column of soil water content per mesocosm. The variable is the absorbance or scattering intensity on the y axis.energy,wavenumbers,scattering vector, and the like are the x axis. - Fit statistics are not variables.
fco2 dry r2,fch4 dry lin, andfn2o dry lin r2record which model a flux came from, linear or exponential, and how well it fitted. - Abbreviations are expanded from the dataset's own data dictionary or
methods text:
hix,bix,fi,sr,suva,lma,pf,pftemp,pfdepth,eh.
Survey names mapped to existing BERVO terms
| Survey names | BERVO term | Note |
|---|---|---|
pfdepth |
Active layer depth of a permafrost soil (BERVO:0001522) |
A probe reading of 120 cm means no permafrost was reached |
avg temperature |
Soil temperature (BERVO:0001477) |
|
c1, c2, fw1, fw2, bw1, bw2 |
Volumetric water content (BERVO:0001743) |
One column per mesocosm in the moisture file |
cnratio |
Plant tissue carbon to nitrogen mass ratio (BERVO:0002055) |
Leaf tissue |
doc … |
Dissolved organic carbon concentration (BERVO:0001670) |
Already defined for soil water |
suva … |
Specific ultraviolet absorbance (BERVO:0002104) |
|
hix … |
Humification index (BERVO:0002109) |
|
fi … |
Fluorescence index (BERVO:0002108) |
|
fco2 dry |
Carbon dioxide flux (BERVO:0001943) |
Chamber flux from soil |
co2 dry mean, ch4 dry mean, n2o dry mean, h2o mean |
Not mapped | Chamber headspace mole fractions and water vapor; see below |
eh … |
Redox potential (BERVO:8000349) |
A concept that carries ODM2:variablename/reductionPotential |
ph … |
pH (BERVO:8000261) |
A concept; BERVO has pH variables for soil, precipitation, irrigation, and wastewater, not for water in general |
ch4 flag, fe flag, hs flag, … |
Quality control flag (BERVO:8000563) |
Six flags |
easting, northing |
Easting (BERVO:8000440), Northing (BERVO:8000441) |
|
normalized absorption |
Absorbance (BERVO:8000236) |
Y axis of the XANES and NEXAFS spectra |
rep |
Biological replicate (BERVO:8000420) |
New terms
Concepts
| New BERVO term | Parent | Cross-reference | From |
|---|---|---|---|
Pore water (BERVO:8001059) |
Environmental material | none; see below | Both porewater datasets |
Permafrost (BERVO:8001060) |
Environmental material | ENVO:00000134 |
Teller 47 |
Iron(II) (BERVO:8001061) |
Ion | CHEBI:29033 |
fe |
Dissolved sulfide (BERVO:8001062) |
Chemical pool | none | hs, sulfide … |
Carbon-13 (BERVO:8001063) |
Isotope | CHEBI:36928 |
delta 13ch4 |
X-ray absorption near edge structure spectroscopy (BERVO:8001064) |
Method | CHMO:0000305 |
Walker Branch |
Small-angle neutron scattering (BERVO:8001065) |
Method | CHMO:0000184 |
Walker Branch |
Fourier transform infrared spectroscopy (BERVO:8001066) |
Method | CHMO:0000636 |
Mesocosms |
Variables
| Survey names | New BERVO term | Parent | BERVO unit | Cross-reference |
|---|---|---|---|---|
lma |
Leaf mass per area (BERVO:0002185) |
Plant trait variable | g.m-2 |
|
c area |
Leaf carbon content per unit area (BERVO:0002186) |
Plant trait variable | g{C}.m-2 |
|
n area |
Leaf nitrogen content per unit area (BERVO:0002187) |
Plant trait variable | g{N}.m-2 |
|
c mass |
Leaf carbon content per unit dry mass (BERVO:0002188) |
Plant trait variable | mg{C}.g-1{dry_mass} |
|
n mass |
Leaf nitrogen content per unit dry mass (BERVO:0002189) |
Plant trait variable | mg{N}.g-1{dry_mass} |
|
pftemp |
Temperature at the top of permafrost (BERVO:0002190) |
Soil heat variable | Cel, K |
|
pf |
Near-surface permafrost presence (BERVO:0002191) |
Soil variable | NA |
|
dic … |
Dissolved inorganic carbon concentration (BERVO:0002192) |
Water quality variable | mg{C}.L-1 |
carbonDissolvedInorganic |
fe, fe … |
Dissolved ferrous iron concentration (BERVO:0002193) |
Water quality variable | umol.L-1 |
|
mn … |
Dissolved manganese concentration (BERVO:0002194) |
Water quality variable | umol.L-1 |
manganeseDissolved |
hs, sulfide … |
Dissolved sulfide concentration (BERVO:0002195) |
Water quality variable | umol.L-1 |
sulfideDissolved |
so4, sulfate … |
Dissolved sulfate concentration (BERVO:0002196) |
Water quality variable | umol.L-1 |
sulfateDissolved |
cl |
Dissolved chloride concentration (BERVO:0002197) |
Water quality variable | umol.L-1 |
chlorideDissolved |
nh4, nh4 … |
Dissolved ammonium concentration (BERVO:0002198) |
Water quality variable | umol.L-1 |
|
nh3 … |
Dissolved ammonia concentration (BERVO:0002199) |
Water quality variable | umol.L-1 |
|
nox … |
Dissolved nitrate plus nitrite concentration (BERVO:0002200) |
Water quality variable | umol.L-1 |
nitrogenDissolvedNitrite_NO2_Nitrate_NO3 |
po4 |
Dissolved orthophosphate concentration (BERVO:0002201) |
Water quality variable | umol.L-1 |
phosphorusOrthophosphateDissolved |
ch4 |
Dissolved methane concentration (BERVO:0002202) |
Water quality variable | umol.L-1 |
methaneDissolved |
bix … |
Biological index (BERVO:0002203) |
Water quality variable | 1 |
|
sr … |
Spectral slope ratio (BERVO:0002204) |
Water quality variable | 1 |
|
fresh … |
Freshness index (BERVO:0002213) |
Water quality variable | 1 |
|
fch4 dry |
Methane flux (BERVO:0002205) |
Surface flux variable | nmol.m-2.s-1, umol.m-2.s-1 |
|
fn2o dry |
Nitrous oxide flux (BERVO:0002206) |
Surface flux variable | nmol.m-2.s-1, umol.m-2.s-1 |
|
delta 13ch4 |
Methane delta carbon-13 (BERVO:0002207) |
Delta carbon-13 | [ppth] |
delta_13COfCH4 |
initial area, final area, raw growth |
Fungal mat area (BERVO:0002208) |
Ecology variable | cm2 |
|
relative growth rate weekly |
Fungal mat relative growth rate (BERVO:0002209) |
Ecology variable | d-1 |
|
colonization status |
Litter colonization status (BERVO:0002210) |
Ecology variable | NA |
|
time to colonization |
Time to litter colonization (BERVO:0002211) |
Ecology variable | d |
|
number dry days week |
Number of dry days (BERVO:0002212) |
Meteorological variable | 1 |
Cross-references in the last column are ODM2 variable names, written in full as
ODM2:variablename/<name>.
Points to note
- Solute variables are for any water. The porewater analytes became
variables measured in Water, not in Pore water, so that one set serves
porewater, stream, and groundwater data alike. Pore water is a concept that
porewater data can name as the medium. The one exception predates this page:
Dissolved organic carbon concentration (
BERVO:0001670) is an EcoSIM variable defined for soil water. - Only ODM2 names that say "dissolved" are cross-referenced. ODM2's
ironFerrous,nitrogen_NH4, andnitrogen_NH3do not say whether the sample was filtered, so they are broader than the BERVO variables and are recorded only in each term'sComment. ODM2 has no names for methane or nitrous oxide flux, biological index, or spectral slope ratio. - Molar units for solutes. Both porewater datasets report solutes in
uMormM, so BERVO usesumol.L-1. The ODM2 nitrogen names are "as nitrogen", which a molar unit makes no difference to. Carbon is the exception: dissolved carbon is conventionally reported by mass, inmg{C}.L-1. - Pore water is not cross-referenced to ENVO. ENVO's interstitial water
(
ENVO:03600009) is defined for rocks and sediments, and BERVO's term also covers soil. - XANES and NEXAFS are one method. CHMO treats them as synonyms. The Walker Branch dataset uses NEXAFS for the carbon K-edge and XANES for the iron and manganese K-edges.
- Chamber headspace concentrations are not added.
co2 dry meanand its methane and nitrous oxide counterparts are dry-air mole fractions inside a closed chamber, an intermediate result in calculating a flux.h2o meanis the water vapor reading from the same analyzer, not soil moisture. - Biological index and freshness index are two variables. Both use excitation at 310 nm and emission at 380 nm. The biological index divides by the emission at 430 nm, and the freshness index (beta:alpha) by the maximum between 420 and 435 nm. The mesocosm dataset reports them in separate columns.
raw growthis a change in Fungal mat area, final minus initial, so it maps to the area variable.- Leaf mass per area is not cross-referenced to specific leaf area
(
TO:0000562), which is its reciprocal.
Stable isotope variables
delta 13ch4 was BERVO's first isotope delta variable, so it came without a
parent. Rather than place one variable under an ill-fitting grouping, the
review of this alignment added the stable isotope deltas from the ODM2
variable names as a family, with the concepts they need.
| BERVO term | Parent | Reference standard (contexts) |
ODM2 variable name |
|---|---|---|---|
Stable isotope variable (BERVO:9000047) |
Variable | ||
Delta carbon-13 (BERVO:0002214) |
Stable isotope variable | Vienna Pee Dee Belemnite | carbon_13StableIsotopeRatioDelta |
Delta deuterium (BERVO:0002215) |
Stable isotope variable | Vienna Standard Mean Ocean Water | hydrogen_2_StableIsotopeRatioDelta |
Delta nitrogen-15 (BERVO:0002216) |
Stable isotope variable | Atmospheric nitrogen standard | nitrogen_15_StableIsotopeRatioDelta |
Delta oxygen-18 (BERVO:0002217) |
Stable isotope variable | none; see below | oxygen_18_StableIsotopeRatioDelta |
Methane delta carbon-13 (BERVO:0002207) |
Delta carbon-13 | Vienna Pee Dee Belemnite | delta_13COfCH4 |
Carbon dioxide delta carbon-13 (BERVO:0002218) |
Delta carbon-13 | Vienna Pee Dee Belemnite | delta_13COfCO2 |
Dissolved inorganic carbon delta carbon-13 (BERVO:0002219) |
Delta carbon-13 | Vienna Pee Dee Belemnite | delta_13COfDIC |
Ethane delta carbon-13 (BERVO:0002220) |
Delta carbon-13 | Vienna Pee Dee Belemnite | delta_13COfC2H6 |
Propane delta carbon-13 (BERVO:0002221) |
Delta carbon-13 | Vienna Pee Dee Belemnite | delta_13COfC3H8 |
Butane delta carbon-13 (BERVO:0002222) |
Delta carbon-13 | Vienna Pee Dee Belemnite | delta_13COfC4H10 |
Water delta oxygen-18 (BERVO:0002223) |
Delta oxygen-18 | Vienna Standard Mean Ocean Water | delta_18OOfH2O |
Water delta deuterium (BERVO:0002224) |
Delta deuterium | Vienna Standard Mean Ocean Water | delta_DOfH2O |
Methane delta deuterium (BERVO:0002225) |
Delta deuterium | Vienna Standard Mean Ocean Water | delta_DOfCH4 |
All take [ppth], UCUM's parts per thousand (per mil), and Isotope delta in
attributes. measurement_ofs names the isotope, and the substance where there
is one.
New concepts:
| BERVO term | Parent | Cross-reference |
|---|---|---|
Isotope delta (BERVO:8001067) |
Relative value | |
Isotope reference standard (BERVO:8001068) |
Concept | |
Vienna Pee Dee Belemnite (BERVO:8001069) |
Isotope reference standard | |
Vienna Standard Mean Ocean Water (BERVO:8001070) |
Isotope reference standard | |
Atmospheric nitrogen standard (BERVO:8001071) |
Isotope reference standard | |
Propane (BERVO:8001072) |
Alkane | CHEBI:32879 |
Butane (BERVO:8001073) |
Alkane | CHEBI:37808 |
- The reference standard goes in
contexts. It is the condition the value is reported under, like Standard ambient temperature on a rate. Delta oxygen-18 names none: it is reported against Vienna Standard Mean Ocean Water for water and against Vienna Pee Dee Belemnite for carbonates and carbon dioxide, and two values incontextswould read as both applying at once. Its definition says which applies when, and Water delta oxygen-18 names its one standard. - Not added: ODM2's
carbon_14andtritium_3H_DeltaTOfH2O. Both isotopes are radioactive and are reported as activities, ages, or tritium units, not as a stable isotope delta, so they belong to a different family.
Survey names left unmapped
| Survey names | Reason |
|---|---|
treatment, phase, site, plot, season |
Experimental design, recorded as metadata |
sampleid, ch4 sample id, fungal mat id |
Identifiers |
species, genus, common name, usda plants symbol, usda citation, fungi species |
Taxonomy |
date, start date, end date, week start, week end, time edt, time est, total weeks, n |
Dates and times; n is days since the mesocosm experiment began |
scattering intensity, scattering vector, energy, wavenumbers |
Spectrum axes |
fco2 dry r2, fco2 dry lin, fco2 dry lin r2, and the methane and nitrous oxide equivalents |
Flux fit statistics |