CalCOFI integrated database release v2026.09.10

Release date: 2026-09-11 · promoted (latest.txt)

The obs objects ship for the last time

v2026.09.06 marked the obs table deprecated, replaced_by: [obs_bio, obs_env], removed_in: next, and this release still exports its 16 partition objects and the single-file obs.parquet twin (401 MB per release beside the pair's 342 MB) because nothing in the notebook acted on the mark. That is deliberate for this cut and final: the next release drops the obs objects and the twin. obs stays as the catalog view over obs_bio + obs_env (views.obs), so cc_get_db() (R and Python) and db-query's __TBL:obs__ keep answering; a reader that resolves the obs table's objects by hand — cc_release_sources(catalog, "obs"), the single_file twin, ducklake/releases/{v}/parquet/obs/ — must move to the pair or the view before then. The list of those readers and their fixes is .claude/plans/2026-09-10 plan_todo — drop the obs objects.md. The hive partitioning of obs_env by measurement_type stays: every browser reader takes the object list from catalog.json, never a glob, and one variable is one ≤ 10 MB object.

The baseline needs five cruises, and the corrected per-sensor CTD series reach obs

Rasmus Swalethorp's review of the transect plotter (2026-09-09) settles two things the release carries:

• climatology keeps a cell only where ≥ 5 distinct cruises contribute (was 3). Measured on v2026.09.06: 577,113 of 768,880 cells survive (75 %; 87 % of the CTD temperature cells, the losses concentrated in the thinly sampled offshore and pre-2004 inshore stations). clim_n and n_cruises stay on every row, so a consumer can show how many observations and cruises made the baseline it subtracts. The calcofi_mets cells (156, none ≥ 5) drop out entirely.
• Ten CTD measurement types become canonical and so reach ctd_thin → obs / obs_env (one hive object each): salinity_1_corr, salinity_2_corr, oxygen_ml_l_{1,2}_sta_corr, oxygen_ml_l_{1,2}_cruise_corr, est_chlorophyll_a_{sta,cruise}_corr, est_nitrate_{sta,cruise}_corr. Until now only the file's own averages (salinity_ave_corr, oxygen_ml_l_ave_sta_corr) and the uncorrected sensors were published, so no consumer could apply the rule Rasmus asked for — the mean of the two corrected sensors, one alone when the other is flagged 8/9, honouring the 1/2 sensor-choice flags — nor offer chlorophyll or nitrate from the bottle-fitted sensor estimates, nor choose between the station- and cruise-corrected fits. The thinned depth set is unchanged (it is derived from the temperature / average-salinity profiles), so these add rows at the depths already kept. Each keeps its own measurement_qual. None carries a variable, so the Explorer's pooled variables do not double-count a sensor beside its average. Sensor-only preliminary cruises stay temperature-only in the plotter (Rasmus: an uncalibrated or drifting sensor reads badly in an anomaly).

Consumers: climatology has fewer rows (a cell absent is an anomaly left blank, never 0); obs_env gains ten measurement_type partitions; metadata/measurement_type.csv flags them is_canonical and declares the oxygen ranges. calcofi4db::combine_sensor_pair() is the tested form of the sensor rule for any consumer.

The climatology and the sections key on the station, not the grid cell

grid_key is a point-in-polygon into the 218 grid cells, and the inshore cells of the core lines are ~2,350 km² boxes holding 2–4 real stations, all occupied every cruise since 2004 (st30-ln90 = 90.30 · 90.28 · 90.27.7 · 88.5/30.1, 3.7 CTD occupations per cruise; st35-ln86.7 3.2; st40-ln83.3 2.9; st25-ln93.3 2.7). climatology was grained on the cell, so the inshore baseline blended stations 15–30 km apart where the gradient is steepest; ctd-transects drew one of them (1,595 of 9,637 CTD occupations, 16.6 %, never drew — 26 % on line 90 since 2004) and the Explorer's Sections lens averaged them. Three products, three answers within 30 km of the coast.

Now (calcofi4db 4.8.0): climatology is grained on site_key (the real station, read from sample), with grid_key kept on the row as the station's modal cell (709 of 9,705 stations straddle a cell edge across their occupations); its primary key and its export sort key follow. site_key itself has one spelling — printf('%05.1f %05.1f', line, station) — applied to every ingest's sample arm by append_sample() and gated at release by check_site_key_format(): v2026.09.06 shipped 28 CTD casts carrying the source's own Sta_ID forms (93.3 26.4, 0093. 060.0, 090.0 27.76, 88.50 030.1) beside the canonical form.

Consumers: climatology gains site_key (first after dataset_key) and keeps every other column; a cell-level reader pools rows by grid_key weighted by clim_n (exactly the old value). ctd-transects (PR site-key), the Explorer's Sections lens (PR site-key) and calcofi4r::cc_climatology() (1.23.0) key on the station; inshore anomalies move by up to ~1 °C at the surface. The 28 CTD site_key values change spelling (same station). Nothing else changes.

Reference layers in spatial_layers.json

The boundary-layer sidecar gains three registry rows with role = reference (calcofi4db 4.8.0, plan 2026-09-09): osm_land (the OpenStreetMap land polygons the Explorer draws over the sea floor and the data, _spatial/osm_land.pmtiles), gebco_gazetteer (219 undersea feature names from the IHO-IOC GEBCO Gazetteer, a label layer) and esri_ocean_reference (a raster row). Every layer now carries role, source_type and source_url; a reference row's n_features / bbox come from reference_layers.json, it has no names and no memberships, and it is not in the spatial table — nothing else in the release changes.

Every released key is declared, and every declared key is measured

The release has always declared its keys in relationships.json and drawn them in the ERD, but it gated only a few: the core primary keys (check_core_pk_unique(), since v2026.08.25's 4,855 duplicate sample_keys) and the cruise_key edges (check_cruise_key_integrity()). The other ~50 declared foreign keys were true by construction and never measured, twelve of the 23 released tables declared no primary key at all (obs_bio, obs_env, sample_root, sample_spatial, climatology, spatial, spatial_attribute, dataset, lookup, taxon_group, the two supplementals), and 28 of the 88 foreign-key rows named thirteen per-dataset tables the release retired in 2026-07 (casts, ctd_cast, zooplankton_tow, …).

Now (calcofi4db 4.7.0): every released table declares a primary key — each measured unique on v2026.09.06 before being declared — relationships.json carries only edges whose both ends ship (the ingest-only rows stay in relationships_all.csv as released = FALSE), and a new integrity.json sidecar beside catalog.json records, per key, rows / distinct / duplicates / NULLs and rows / NULL / orphans, with ok overall. A duplicate or NULL primary key or any foreign-key orphan stops the release (release_database.qmd relationship_integrity, after every released table exists), and test_release.qmd refuses to promote a release without an all-ok integrity.json. A NULL foreign key is a nullable edge (an env row's taxon_key, an ungridded sample's grid_key), not an orphan. metadata/release_tables.csv describes sample_root and sample_spatial at last (both were absent from metadata.json, so the schema browser could not list them) and drops the retired obs_freq row.

Thirteen edges the release always had but never declared are declared now, each measured at 0 orphans first (spatial_attribute → spatial, cruise → ship, the supplementals' cruise_key / grid_key / dataset_key / measurement_type, sample_root's three, sample_spatial.root_id, obs_attribute.dataset_key). One is deliberately not: obs_mets_full.sample_key → sample resolves for 73,607 of its 2,168,850 distinct keys — sample holds the 77,795 underway events the METS headline series keys to, while the full-resolution table mints one key per record that never reaches sample. Declaring it would fail the release on 18,990,343 orphans; leaving it undeclared hides a real gap, so it is recorded here and as a workflows issue for the METS ingest until the supplemental's events either join sample or carry a documented per-record key.

Consumers: relationships.json lists fewer, truer edges (the 60 with both ends released, deduplicated, plus the thirteen above) and a primary key for every table; integrity.json is new and optional to read; metadata.json gains sample_root and sample_spatial. Nothing in the parquet changes.

A publisher re-run over a frozen release costs a hash comparison, not a rebuild

The four generic publishers now check before they build or upload, so they can sit in the regular targets run without regenerating identical outputs (2026-09-06):

• publish_to-netcdf.qmd: a file whose db_release attribute names this release and that the published manifest already lists is returned, not rebuilt; cc_netcdf_plan() recognises a version already published with these bytes and cc_netcdf_publish() then writes nothing — before, every render rebuilt every file (the CTD supplemental is an hour and 3.6 GB) and re-wrote manifests.json with a new generated_utc.
• publish_to-erddap.qmd: the config header carries the release date, not the render date, so an unchanged config is unchanged; only datasets whose definition changed (or are new) are flagged for reload, where every one of 34 was flagged each run.
• publish_to-obis.qmd: an archive already built for this release is reused; the zip itself is now byte-stable (members stamped with the release date, calcofi4db 4.6.2) and the manifest's generated_utc moves only when the content hash does.
• publish_to-edi.qmd: a package already built for this release is reused; the export pins DuckDB's insertion order so the hashed CSVs are a function of the release objects.
• Every upload goes through put_gcs_file(skip_unchanged = TRUE) (calcofi4db 4.6.1): an object with the same MD5 is not sent again.

Portal bundles are staged where a reviewer can see them

publish_to-obis.qmd and publish_to-edi.qmd (both first run against v2026.09.06) now copy what they build to the public bucket at a deterministic address before any deposit — gs://calcofi-db/publish/dwca/{dataset_key}/{dataset_key}_{version}.zip (+ manifest) and gs://calcofi-db/publish/edi/{dataset_key}/{dataset_key}_{version}/ — so a provider, and the dataset page (Archives & portals, "built, not deposited"), can inspect a bundle before it goes to the IPT or PASTA. The deposit itself stays a deliberate act (Decision 21; CALCOFI_PUBLISH_EDI).

Dataset colours are re-spread so every dataset reads apart

The sixteen dataset.color values (each ingest_*.qmd front matter dataset_meta.color, carried by the dataset table and datasets.json) were chosen one at a time as pastel tints. Measured on 2026-09-09 with a palette validator over all pairs: the two closest biology datasets were ΔE 4.3 apart for normal vision and 1 under deuteranopia, fifteen sat above the lightness band and thirteen under 3 : 1 on white. They are now one set found by search over OKLCH inside the band the light and dark themes share (L 0.48–0.665, chroma ≥ 0.106), maximising the worst within-realm pair — biology 13.6 normal / 7 CVD, environment 14.7 / 8 — then the worst cross-realm pair (7.9), then assigned so that the datasets that appear together (cufes and ichthyo, ZooDB and ZooScan, bottle and CTD …) are far apart; every colour is ≥ 3 : 1 on white and on navy. A dataset's name still travels beside its dot everywhere: twelve colours in one band cannot all clear the validator's normal-vision floor (a packing bound), so colour stays a secondary cue by design.

Consumers: the landing page, the Explorer, db-viz-station and the docs read the release's colour and follow on their next build; screenshots change; nothing is keyed on a hex.

Every observed taxon has a record: taxa.json, the species catalog

The release has shipped the taxon table since v2026.07 and counted it on calcofi.io as "2,614 taxa". That is the size of a lookup table, not a number of organisms: 1,108 of its rows have no observation at all — 904 are lineage ancestors (Biota, Animalia, Chordata …) and 204 are entries in a dataset's vocabulary the sampling never met. The observed count on v2026.09.06 is 1,506, and 1,008 of those are identified to species; the remaining 498 stopped at genus, family, order or class (Sebastes 18,187 rows, "Unidentified teleost" 72,797). Nothing published the lineage, the per-year counts or the crosswalk, so no page could say which species a dataset holds.

New sidecar taxa.json beside datasets.json (calcofi4db 4.9.0 build_taxa_catalog(), schema taxa.schema.json 1.0, ~2.4 MB). One entry per taxon row with an observation at or below it — the 1,506 observed plus their 904 ancestors, 2,410 entries — each carrying its accepted name and common name, rank and taxonomic status, the WoRMS · ITIS · GBIF · NCBI · iNaturalist ids, the parent_taxon_key and the flattened lineage, its taxon_group memberships, direct{} (the observations keyed to it) and rollup{} (it and every descendant: observations, taxa, species, datasets, year span), and one block per dataset that observed it — observations, samples, years, per-year counts, life stages — ending in sources[], the dataset_taxon rows that resolve to it: what that dataset calls the taxon, flagged synonym, sp_to_genus (a "… sp." name resolved to its genus), rekeyed, id_conflict or no_name (a code only). Measured over v2026.09.06's 1,917 dataset_taxon rows: 1,704 use the accepted name, 120 carry only a code, 93 use a different name.

The two id flags say different things, and the difference matters on a page. A taxon is keyed by exactly one authority; only a disagreement there is a re-key. 27 rows are rekeyed, all Farallon — an ITIS TSN the source gave that ITIS itself has deprecated, the row keyed to the successor (taxon.notes: "itis:174550 deprecated in ITIS -> itis:1255048"). 27 are id_conflict, all ichthyoplankton — worms:-keyed taxa whose source ITIS hint differs from the itis_id WoRMS publishes as its external link (taxon.notes: "2026-08-05: itis_id 622362 via WoRMS external link"). Nothing was re-keyed in those 27: two authorities' crosswalks disagree, and that is what the pill says. datasets[] lists the ten datasets carrying taxa with their catalog colour and, per dataset, the vocabulary rows that have no observation anywhere — the list a provider wants and no page had.

The record is generated and gated. check_taxa_catalog() re-measures every count against the release's own obs_bio, requires every parent_taxon_key to resolve inside the record (a page with a dangling breadcrumb is a 404), requires the roots' rollups to sum to obs_bio's 1,257,902 keyed rows, and requires unique page slugs and known datasets and flags; release_database.qmd step 3b′ stops the release on any failure and test_release.qmd refuses to promote without an all-pass taxa_catalog gate. taxa.json joins RELEASE_REQUIRED_OBJECTS, so a release that does not carry it cannot be promoted.

Consumers: additive — no existing object, table or column changes. calcofi.io/species/ is generated from this file (one page per taxon_key, at /species/{key with ':' written '-'}/); the landing page's Life tile and numbers band read its counts. A consumer that wants the crosswalk reads taxa[].datasets[].sources[] instead of joining dataset_taxon by hand.

Five bottle series declare their physical bounds, and eleven impossible values leave

calcofi_bottle declared no bound on any of its 26 series, so v2026.09.06 published a 99.00 °C and a 56.87 °C at 50 m (2020-07-33P4, station 93.3/30 — the same two bottles read 9.50 and 21.06 PSU), six potential densities of 216–251 kg/m³ (2014-11-32NM, 2015-04-32NM) and one surface oxygen of −200.2 ml/L / −8,740.6 µmol/kg / −3,605 % saturation (2020-07-33P4, station 90/30). ingest_calcofi_bottle.qmd § Declare and Enforce Physical Bounds now declares temperature −2…40 °C and sigma_theta 15…35 kg/m³ (the CTD's own bounds for the same quantities) and oxygen_ml_l −0.5…15, oxygen_umol_kg −20…700, oxygen_saturation −1…250 — the oxygen floors just below zero so the four Winkler zeros of the line 83.3 oxygen minimum (−0.010 ml/L, 550–570 m, 1995–2002) stay — and drop_out_of_bounds() removes the eleven rows before obs is emitted, as the CTD and METS ingests already do. This was not a DBF-era 9-fill: no bottle series carries a −99 / 999 pattern, and the 1,739 temperatures at exactly 9 or 99 are 9.0 °C readings. Salinity declares nothing yet — cruise 2021-05-3322 reads 24.19–27.06 PSU in 918 bottles to 568 m across 39 stations (Q13, high), a whole cruise the provider must rule on before any floor is set. Consumers: obs_env loses 11 calcofi_bottle rows; measurement_type.valid_min / valid_max are populated for the five series and check_measurement_bounds() treats them as declared.

A label per crosswalk key: metadata/variable.csv

measurement_type.variable has said which raw series measure the same thing since 4.6.0, but there was nowhere to put a name for the key itself — only description on each member row, a column note ("DO average station-corrected"). New registry metadata/variable.csv (variable, label, description, units, nerc_p01, category, is_unified; calcofi4db read_variable() / register_variables() / check_variable_registry(), mirroring the measurement_type.csv helpers) carries one row per key the release carries with variable set. Seeded with the five pairs the Explorer's UNIFIED already carries — temperature, salinity, oxygen_ml_l, oxygen_umol_kg, sigma_theta — checked against D3's crosswalk rule (identical NERC P01 · same units or a declared conversion · same kind of sample · not plausibly the same physical samples) by the new, reproducible libs/measure_variable_crosswalk.R: of the 15 NERC P01 concepts shared by more than one released env series (84 series, 5 datasets, v2026.09.06), only these four pass all four criteria outright.

sigma_theta is the fifth and, measured strictly, does not: the bottle's own computation carries NERC P01 SIGTEQ01 ("by computation from salinity and potential temperature") while the CTD's carries SIGTPR01 ("by CTD and computation …") — two different concepts for the same physical quantity. variable.csv's sigma_theta row therefore declares no nerc_p01 rather than picking a side, the same exact-match rule as everywhere else in these registries; register_variables() and check_variable_registry() both refuse a row whose nerc_p01 disagrees with a member series' own value, so this could not have been filled in by mistake. Everything else the crosswalk touches stays apart: the CTD's own embedded btl_* bottle table (nitrate, nitrite, phosphate, silicate, ammonium, phaeopigment, depth, chlorophyll, temperature) shares a P01 with the bottle dataset's series but fails criterion (iv) — measured, 5,061 of calcofi_bottle's 8,352 casts 1993–2021 (60.6%) have a matching calcofi_ctd-cast cast at the same site_key within one hour (5,061 of 16,431 CTD casts, 30.8%), plausibly the same physical bottles. The bottle's alkalinity_rep1 / dic_rep1 replicates and DIC's alkalinity / dic means share a P01 too but fail criterion (iii) (replicate vs mean); two proposed questions ask the DIC provider whether the bottle's replicate is one of the two analyses averaged into the reported value (calcofi_dic_08, calcofi_dic_09). Consumers: additive — a new registry file and three new calcofi4db functions; coverage.json's variables[] gains label from this registry at the next step (WS-M2).

Six underway and CTD series declare their physical bounds; the 9,895 °C sea surface and the PAR fills leave

v2026.09.06 published a sea-surface temperature of 9,895 °C (calcofi_mets sst_c: three readings of 9,231–9,895 °C on 2016-07-32I1), an intake flow of exactly −99 L/min beside 39 smaller negatives (uws_flow, 2016), fourteen negative bottom depths (bottom_depth_m, five cruises 2020–2022), a thermosalinograph salinity of 45.6 PSU (tsg1_salinity_psu), and from the CTD files a surface PAR (spar) running from −3.07 × 10¹⁷ to 2.01 × 10¹⁶ µE/m²/s — 31,623 values on ten cruises 1995–2008, 6 % of the series — and an in-water PAR (par) with 34,233 values at exactly 9999, a fill, plus 1,065 more above 5,000 and eight below −100 (24 cruises, 1994–2025). None of the six series declared a bound, so nothing caught any of it; the measurements catalog (below) surfaced them on 2026-09-10 and Ben ruled them a certain bug, not a question. ingest_calcofi_mets.qmd now declares sst_c −2…40 °C, tsg1_salinity_psu 0…45 PSU and bottom_depth_m 0…11,000 m (the registry's own bounds for the same quantities on other series) and uws_flow ≥ 0; ingest_calcofi_ctd-cast.qmd declares par and spar −100…5,000 µE/m²/s (the sun delivers ~2,500 at the top of the atmosphere; a dark reading sits within a few units of zero). Both ingests already ran drop_out_of_bounds() against the registry, so the values leave at the ingest and each now asserts nothing remains outside a declared bound. Not bounded, and noted for the provider: sss_psu reads below 20 PSU on a quarter of its rows (a flushed intake, not a sentinel), rel_humidity_pct reaches 120 %, and the CTD's beam_attenuation / transmissometer carry calibration negatives. Consumers: obs_env loses 3 + 40 + 14 + 2 calcofi_mets rows and 31,623 + 35,306 calcofi_ctd-cast rows at the release grain (the full-resolution obs_mets_full / obs_ctd_full lose more; the ingests report the count); measurement_type.valid_min / valid_max are populated for the six series; the measurements catalog reports a series' observed range within its declared bounds and counts what fell outside.

Every released measurement has a record: measurements.json, the measurements catalog

The release writes one more sidecar beside taxa.json: measurements.json, the environment half of the catalog (plan 2026-09-10 § D2/D4, Appendix A; calcofi4db::build_measurements_catalog(), schema measurements.schema.json 1.0). One entry per measurement key obs_env carries — the registry's variable where one is set, so the bottle's temperature and the CTD's temperature_ave are one page, else the measurement_type — and under it one series[] per measurement_type × dataset with that dataset's own source column and flag column, its values by year, calendar month, eight depth bands and quality code, the observed min / 5th / median / 95th / max, the registry's declared bounds and the NERC P01 / P06 ids. Measured on v2026.09.06: 79 measurements over 84 series in 5 datasets, 25,006,583 values (Physical Oceanography 39 · Productivity & Pigments 14 · Nutrients & Chemistry 12 · Carbonate System 6 · Meteorology & Sea State 4 · Picoplankton & Bacteria 4), 167 KB; counts.full_rows adds the two full-resolution supplementals for the 316,328,163 the front door's band counts. A registry row that never reaches obs_env from a supplemental's own source table — a raw CTD sensor, a thermosalinograph past the first — gets no page and is listed under its dataset in full_resolution_only[] with the table it does live in (21 for the CTD files, 37 for METS, none elsewhere). related[] names the other keys sharing a NERC P01 concept that are kept apart on purpose, with the reason — all 76 directed pairs carry one (same_bottles 36 · underway_vs_cast 16 · sensor_vs_mean 8 · pre_qc_twin 6 · replicate_vs_mean 4 · paired_sensors 4 · same_casts 2): P01 identity says two series name the same quantity, never that they may be pooled — the CTD files' own btl_* bottle table is plausibly the same physical bottles as the bottle dataset. A series' observed{} is computed within its declared bounds and what falls outside is counted in out_of_bounds{n, min, max}, so a page shows the range a reader would use while the breach stays visible: the bottle's temperature reads 1.44–31.14 °C with out_of_bounds {n: 2, min: 56.87, max: 99.00}, its sigma_theta 16.996–28.139 kg/m³ with six values of 216.6–250.8, METS sst_c 0.007–25.89 °C with three of 9,231–9,895, and CTD par / spar 4,997 µE/m²/s with 35,306 and 31,623 outside — the rows the two bounds entries above drop at the ingest, still present in v2026.09.06 and now stated rather than averaged into a page's range. Thirteen series carry sentinel_suspected (a declared bound broken, or — where nothing is declared — an extreme both past ±99 and 100× the series' own 5th/95th percentile, which is what catches the bottle's r_oxygen_umol_kg at −8,740 and the CTD's specific_volume_anomaly at −63,921); 18 series still declare no bound at all. The raw counts are untouched, so the arithmetic gate still equals obs_env's row count. Nothing on a measurement page is authored: the label comes from metadata/variable.csv and, absent a row, falls back to the canonical series' registry description carrying a no_label flag. measurements.json joins RELEASE_REQUIRED_OBJECTS and a measurements_catalog gate in test_release.qmd feeds the promote gate — schema valid, the counts re-measured against this release's own obs_env, and the sum of series[].n_values over every key equal to obs_env's row count, which is what catches a series counted twice. Consumers: calcofi.io reads it to generate /measurements/ and one page per key (the landing page's Measurements index); coverage.json's variables[] gains a label field from metadata/variable.csv — filled for the five unified keys, which the CalCOFI Explorer may read in place of its hard-coded UNIFIED labels — and valid_min / valid_max from the registry so a ramp or an axis can be clipped at first paint. Five of the 79 measurements carry an authored label; the other 74 fall back to their canonical series' description with a no_label flag. No released table, column or row changes.

Contents (generated)

23 tables, 356,635,055 rows, 2.58 GB.

Datasets (16): calcofi_bottle, calcofi_ctd-cast, calcofi_dic, calcofi_mets, calcofi_phyllosoma, calcofi_phytoplankton, cce-lter_euphausiids, cce-lter_picoplankton-bacteria, cce-lter_zoodb, cce-lter_zooscan, cdfw_dungeness-crab, farallon_bird-mammal, sio_mesopelagic-fish, sio_pic-zooplankton, swfsc_cufes, swfsc_ichthyo

Validation: 87 pass / 0 fail / 4 skip (consumer-contract suite, 2026-09-10T22:37:26Z).

How to cite

CalCOFI (2026). CalCOFI Integrated Database, release v2026.09.10 [Data set]. Scripps Institution of Oceanography, NOAA Fisheries, and California Department of Fish and Wildlife. https://doi.org/10.5281/zenodo.22698724

Cite the source datasets you use alongside the release:

• calcofi_bottle — CalCOFI. (2023). CalCOFI Bottle Database 194903-202105. CalCOFI.org. · license pending
• calcofi_ctd-cast — CalCOFI. (2023). CalCOFI CTD Cast Files. CalCOFI.org. · license pending
• calcofi_dic — Keeling, C.D.; Lueker, T.J.; Emanuele, G.; Dickson, A.G.; Martz, T.R.; Wolfe, W.H.; Mau, A. (2025). Discrete profile dissolved inorganic carbon, total alkalinity, water temperature and salinity measurements for CalCOFI (NCEI Accession 0301029). NOAA NCEI. https://doi.org/10.25921/3w9f-jd72 · CC-BY-4.0
• calcofi_mets — CalCOFI. Underway (METS) TSG/Meteorology Data. CalCOFI.org. · license pending
• calcofi_phyllosoma — CalCOFI - Scripps Institution of Oceanography and T. Koslow. 2017. Data pertaining to lobster phyllosoma, Panulirus interruptus, collection methods, locations, identification and staging (1951-2008, months of July and August) ver 4. Environmental Data Initiative. https://doi.org/10.6073/pasta/9e38121ebb26f1b59b7b39b2eff844fa · custom (https://portal.edirepository.org/nis/metadataviewer?packageid=knb-lter-cce.188.4)
• calcofi_phytoplankton — CalCOFI - Scripps Institution of Oceanography, California Current Ecosystem LTER, and E. Venrick. 2023. Temporal and spatial changes of the abundance and species composition of phytoplankton in the California Current from samples collected aboard CalCOFI cruises from summer 1996 through 2022. ver 4. Environmental Data Initiative. https://doi.org/10.6073/pasta/60edabfbfd85c623fce05822befaa071 · CC0-1.0 (https://creativecommons.org/publicdomain/zero/1.0/)
• cce-lter_euphausiids — Ohman, M.D. 2022. California Current Ecosystem Euphausiid data, Brinton and Townsend Euphausiid Database (BTEDB) ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/4a92a0044bcd1523a4f994ece874a57d · custom (https://portal.edirepository.org/nis/metadataviewer?packageid=knb-lter-cce.313.1)
• cce-lter_picoplankton-bacteria — Landry, M. (2004-2023). Picoplankton and Bacteria Abundance (CalCOFI Cruise). CCE LTER. · license pending
• cce-lter_zoodb — citation pending · custom (https://oceaninformatics.ucsd.edu/zoodb/)
• cce-lter_zooscan — citation pending · custom (https://oceaninformatics.ucsd.edu/zooscandb/)
• cdfw_dungeness-crab — Rogers-Bennett, L.; Jones, E.; Klemmedson, A. (2026). CDFW Dungeness Crab Megalopae from archived CalCOFI plankton samples (1949-2014). California Department of Fish and Wildlife, published through CalCOFI / Scripps Institution of Oceanography. · CC-BY-4.0
• farallon_bird-mammal — citation pending · custom (https://oceanview.pfeg.noaa.gov/CalCOFI/app/resources/docs/Data_Sharing_Agreement_FarallonInstitute.pdf)
• sio_mesopelagic-fish — Koslow, J. Anthony (2016). CalCOFI Trawl Data. In California Cooperative Oceanic Fisheries Investigations (CalCOFI): Acoustic and Trawl Data. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0BZ64DH · CC-BY-4.0
• sio_pic-zooplankton — citation pending · license pending
• swfsc_cufes — citation pending · custom (https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFIcufes.das)
• swfsc_ichthyo — NOAA Fisheries SWFSC. CalCOFI Ichthyoplankton Database. · license pending

Access

con <- calcofi4r::cc_get_db(version = "v2026.09.10")

con = calcofi4py.cc_get_db("v2026.09.10")

Parquet: https://storage.googleapis.com/calcofi-db/ducklake/releases/v2026.09.10/parquet/{table}.parquet; full history: RELEASES.md.