Phaeopigment measured fluorometrically
- 245,665
- values
- 613
- flagged
i
613 of these 245,665 values (0.2 %) are flagged by their provider as questionable or bad. The Explorer, the climatology and its anomalies leave them out; do the same when you read the data yourself (cc_qual_ok_sql()in calcofi4r,qual_ok_sql()in calcofi4py). - 13,934
- sampling events
- 1973–2021
- years
- 1
- dataset
- 0–1,122 m
- depth
- every month
- seasons
Filtration and analysis protocols unspecified.
Filter, 90% acetone extraction, benchtop fluorometer
Bottle sampling methods on calcofi.org ↗EOV Phytoplankton biomass and diversity
CalCOFI holds 245,665 values of it from 13,934 sampling events in one dataset, 1973–2021, from the surface to 1,122 m. At 10–50 m it has fallen 0.01 per decade since 1984.R Phaeopigment is chlorophyll after something has eaten it or it has died, so the ratio of the two is a reading of how fast the grazers are working through the bloom.C
other ways to say why · 2
- It is also the reason chlorophyll is read twice, before and after acid: the acid makes the same change in the tube that grazing makes in the sea. needs a citation before it can be the pick
- Wikipedia Pheophytin or phaeophytin is a chemical compound that serves as the first electron carrier intermediate in the electron transfer pathway of Photosystem II in plants, and the type II photosynthetic reaction center found in purple bacteria. In both PS II and RC P870, light drives electrons from the reaction center through pheophytin, which then passes the electrons to a quinone (QA) in RC P870 and RC P680. Pheophytin · CC BY-SA 4.0 · rev. 1373850179
The measurement
Measured in i
One row per series, one cell per year, darker with more values — the same strip the front
door draws per dataset and a species page draws per taxon. Each row is one dataset's own
measurement_type; the label is written once, in the title above.
i
One row per series, one cell per year, darker with more values — the same strip the front door draws per dataset and a species page draws per taxon. Each row is one dataset's own measurement_type; the label is written once, in the title above.
-
series
phaeopigment· source columnphaeop· flag columnphaqua613 flagged · 0.2 %
The structure
RDKit 2026.03.6 from the ChEBI molfile, in the page’s ink · CC BY 4.0. ChEBI’s roles are never shown.
How it is measured
A known volume filtered onto a GF/F filter, cold-extracted in 90% acetone for 24-48 hours and read on a fluorometer; the extract is then acidified, which strips the magnesium and turns chlorophyll into phaeopigment, and read again (Yentsch & Menzel 1963; Holm-Hansen et al. 1965; Lorenzen 1967). (calcofi.org Bottle sampling methods)
Bottle sampling methods on calcofi.org ↗Why it matters
The familiar scale i
Bars are each series' 5th–95th percentile, the line its minimum to maximum, the ring its median;
the marks are metadata/measurement_scale.csv's, each hovering to its own source.
i
Bars are each series' 5th–95th percentile, the line its minimum to maximum, the ring its median;
the marks are metadata/measurement_scale.csv's, each hovering to its own source.
The record’s own history i
Deeper than the climatology reaches: 49 values at 500–1000 m, 26 values at 1000–2000 m have no
normal to depart from, because the release’s climatology stops at its
deepest built bin. Carrying it to the bottom is one argument of
build_climatology() and puts these bands on the page too.
i
Deeper than the climatology reaches: 49 values at 500–1000 m, 26 values at 1000–2000 m have no
normal to depart from, because the release’s climatology stops at its
deepest built bin. Carrying it to the bottom is one argument of
build_climatology() and puts these bands on the page too.
the GOOS specification sheet for this Essential Ocean Variable lists it
The record
Ways in i
Read from measurements.json of release
v2026.10.14, written at release by
calcofi4db::build_measurements_catalog() beside
taxa.json. The catalog's index is
/measurements/; the JSON-LD on this page is a
schema.org/DefinedTerm in the NERC P01 term set with a
PropertyValue per series.
ExplorerExplorer · a depth section vs normaldb-queryi
Read from measurements.json of release v2026.10.14, written at release by calcofi4db::build_measurements_catalog() beside taxa.json. The catalog's index is /measurements/; the JSON-LD on this page is a schema.org/DefinedTerm in the NERC P01 term set with a PropertyValue per series.
SELECT * FROM read_json('…/v2026.10.14/catalog.json')
-- objects[] WHERE table = 'obs_env'
-- AND partition_value = 'phaeopigment'library(calcofi4r)
con <- cc_get_db() # the promoted release
tbl(con, "obs_env") |> filter(measurement_type %in% c("phaeopigment"))import calcofi4py as cc
con = cc.cc_get_db()
con.sql("SELECT * FROM obs_env WHERE measurement_type IN ('phaeopigment')").df()By depth i
Values per depth band at the release grain, one thin bar per series. The bands are the
record's own (0-10 … 2000+ m).
i
Values per depth band at the release grain, one thin bar per series. The bands are the record's own (0-10 … 2000+ m).
By month i
Values per calendar month, one row per series: CalCOFI's quarterly cruises show as peaks in
the months the ships sail.
i
Values per calendar month, one row per series: CalCOFI's quarterly cruises show as peaks in the months the ships sail.
Range & quality
details
- bounds
- The registry declares
at least -5 µg/Lforphaeopigment; a value outside it is dropped at the ingest (drop_out_of_bounds()). - observed
- Hydrographic Bottle
phaeopigment-3.89 · median 0.11 · 65.3 µg/L (5th–95th percentile 0.02–0.605) - flags
- Hydrographic Bottle
phaeopigmentphaquaon 613 of 245,665 rows:8100 ·9513; qual_ok keeps 245,052. The codes are this dataset's own vocabulary, uninterpreted. - baseline
- A monthly climatology exists for this measurement (the release's climatology table: 1993–2013, dataset × station × the cruise's month × 10 m bin), so the Explorer can draw anomalies against it rather than values.
Related measurements i
The same quantity from another platform or another kind of sample, each its own page and
never merged into this one: a dataset's own bottle samples would count that dataset twice, an underway intake
is not a cast, and a replicate is not a mean. The reason is the record's
(related[].why).
i
The same quantity from another platform or another kind of sample, each its own page and never merged into this one: a dataset's own bottle samples would count that dataset twice, an underway intake is not a cast, and a replicate is not a mean. The reason is the record's (related[].why).
- Bottle phaeopigment btl_phaeopigment · CTD Cast Files · 1993–2026 · 113,138 values · P01 PHAEZZXX the same quantity from the CTD files' own bottle samples — plausibly the same physical bottles, so merging them would count the bottle dataset twice
Cite
Cite the release; each dataset's own citation, licence and DOI are on its page — Hydrographic Bottle. The Explorer's Share → Cite writes it for the view you make.