Source portal: ZooDB (SIO Ocean Informatics / Mark Ohman Lab / SIO Pelagic
Invertebrate Collection) — https://oceaninformatics.ucsd.edu/zoodb/
Access: public login (name/email), save.php CSV export endpoint.
Downloaded: 2026-06-26 by CalCOFI data integration (issue CalCOFI/workflows#31).
Query parameters (held constant across all files)
| param | value | meaning |
|---|---|---|
beginYear / endYear |
1949 / 2026 | full temporal range |
month[] |
1–12 | all months |
timeType |
all |
day + night |
locType |
all |
all locations |
GS[] |
.* |
all genera/species within the higher taxon |
PS[] |
.* |
all phases/stages combined |
pooled |
combined |
returns BOTH unpooled tows and pooled region-aggregates (see Source column) |
calcType |
individual |
one value per sample (no temporal mean) |
corrected |
(off) | RAW counts, net correction factor NOT applied |
questionableID |
(off) | excludes questionable identifications |
calcUnit |
1000m3 / m2 |
one file each per taxon |
HT[] |
one higher-taxon per file | 33 taxa + .* (all-taxa total) |
Files: {taxon_slug}__{1000m3|m2}.csv (33 taxa × 2 units) plus
_all_taxa__{unit}.csv (community total, QA reference). See _manifest.csv
for per-file HTTP code, byte size, and unpooled/pooled row counts.
Semantics (important for ingest)
- One row = the taxon was analyzed for that sample.
Abundance = 0means analyzed-but-absent; a missing taxon×sample means not analyzed (coverage differs by taxon/cruise — do NOT impute zeros). Biomass(mg C / m²) is unit-independent — identical in the1000m3andm2files; onlyAbundancechanges withcalcUnit.Source=Unpooled(single net tow, has Line/Station/lat/lon/datetime) orPooled(region aggregate of N tows per cruise; Line/Station/position = N/A,Tows= number pooled).
Snapshot note
The live ZooDB is flagged "WORK IN PROGRESS: not yet complete." This snapshot's
all-taxa unpooled count (225 tows) differs from an earlier 2026-06-19 manual
export (276 tows) — plausibly euphausiids (a separate database, ingested via
ingest_cce-lter_euphausiids) were split out of the holoplankton "all
taxonomies" aggregate. Treat this directory as a single self-consistent snapshot.