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Ohman", "Marina Frants"], "creators": [], "funding": null, "source_accessed": "2026-09-04" }, "links": { "calcofi_org": "https://calcofi.org/data/marine-ecosystem-data/zooplankton/", "data_source": "https://oceaninformatics.ucsd.edu/zooscandb/", "workflow": "https://calcofi.io/workflows/ingest_cce-lter_zooscan.html", "page": "https://calcofi.io/datasets/cce-lter_zooscan/" }, "coverage": { "realm": "bio", "temporal": "2005-07 to 2026-04", "year_min": 2005, "year_max": 2026, "years": [ { "year": 2005, "n_obs": 3062, "n_roots": 36 }, { "year": 2006, "n_obs": 6450, "n_roots": 76 }, { "year": 2007, "n_obs": 5584, "n_roots": 66 }, { "year": 2008, "n_obs": 5384, "n_roots": 64 }, { "year": 2009, "n_obs": 6560, "n_roots": 77 }, { "year": 2010, "n_obs": 6132, "n_roots": 72 }, { "year": 2011, "n_obs": 6632, "n_roots": 80 }, { "year": 2012, "n_obs": 4638, "n_roots": 54 }, { "year": 2013, "n_obs": 6290, "n_roots": 73 }, { "year": 2014, "n_obs": 5892, "n_roots": 68 }, { "year": 2015, "n_obs": 6684, "n_roots": 78 }, { "year": 2016, "n_obs": 5202, "n_roots": 60 }, { "year": 2017, "n_obs": 6298, "n_roots": 75 }, { "year": 2018, "n_obs": 6404, "n_roots": 77 }, { "year": 2019, "n_obs": 6144, "n_roots": 75 }, { "year": 2020, "n_obs": 4804, "n_roots": 59 }, { "year": 2021, "n_obs": 6472, "n_roots": 77 }, { "year": 2022, "n_obs": 4498, "n_roots": 51 }, { "year": 2023, "n_obs": 6814, "n_roots": 77 }, { "year": 2024, "n_obs": 7020, "n_roots": 79 }, { "year": 2025, "n_obs": 7414, "n_roots": 83 }, { "year": 2026, "n_obs": 2314, "n_roots": 26 } ], "spatial": "30.4–34.5°N, 124.0–117.8°W", "bbox": { "lat_min": 30.42, "lat_max": 34.45, "lon_min": -124, "lon_max": -117.77 }, "n_obs": 126692, "n_roots": 1483, "n_stations": 19, "n_variables": 4, "n_taxa": 23, "depth_min_m": 0, "depth_max_m": 220, "variables": ["zooscan_abundance", "zooscan_biomass_carbon", "zooscan_carbon_individual", "zooscan_feret_diameter"], "life_stages": [], "contributes_to": [] }, "tables": ["sample", "obs", "taxon", "dataset_taxon", "measurement_type"], "objects": [ { "table": "obs", "scope": "partition", "shared": false, "path": "ducklake-staging/tables/obs/dataset_key=cce-lter_zooscan/8767afb6413867e98cfceee3/data_0.parquet", "url": "https://storage.googleapis.com/calcofi-db/ducklake-staging/tables/obs/dataset_key=cce-lter_zooscan/8767afb6413867e98cfceee3/data_0.parquet", "bytes": 636768, "sha256": "a47319cbb94471d72e13561cc89a80dd0410c36c21179ce4c42c4ae8dd32d979", "since": "v2026.09.04" } ], "since_version": "v2026.08.25", "distributions": [ { "kind": "download", "url": "https://storage.googleapis.com/calcofi-db/ducklake-staging/tables/obs/dataset_key=cce-lter_zooscan/8767afb6413867e98cfceee3/data_0.parquet", "format": "parquet", "table": "obs", "scope": "partition", "shared": false, "title": "obs (this dataset's rows)", "bytes": 636768, "sha256": "a47319cbb94471d72e13561cc89a80dd0410c36c21179ce4c42c4ae8dd32d979", "since": "v2026.09.04", "status": "current" }, { "kind": "download", "url": "https://storage.calcofi.io/calcofi-files-public/netcdf/cce-lter_zooscan/v2026.09.04/cce-lter_zooscan.nc", "format": "netcdf", "id": "cce-lter_zooscan", "title": "CF netCDF", "bytes": 13116659, "sha256": "b734e22ed72d1f48092f8861e940885e3697acf4b449990c0d02f74694f8297a", "cf_scope": "Fully CF: each row is an independent observation with its own time and position, which is a CF point collection. Rows are at the OCCURRENCE grain (event x taxon x life stage x depth), not the event grain, so a sample with many taxa contributes many points. 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Two efforts: a 2008-2014 time series of 310 sorted samples (A. Klemmedson, 2015) yielding 24 M. magister megalopae from 14 samples, and 216 archived samples from the 1949-2009 sorting log that were examined and found free of M. magister (1984-2009, E. Jones, as of 2012-02-15). Only examined samples are published — the log's remaining unsorted rows are a fact of the archive's inventory, not a sample of this dataset. Spring cruises, CalBOBL oblique tows, lines < 80 / stations < 90. Counts are occurrence in the examined aliquot, not standardized density. Sorting was performed at the SIO Pelagic Invertebrate Collection, where the removed megalopae are archived in vials.\n", "keywords": ["EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > AQUATIC ECOSYSTEMS > PLANKTON > ZOOPLANKTON", "EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > DECAPODS"], "attribution": { "citation_main": "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.\n", "citation_others": [], "doi": null, "license": "CC-BY-4.0", "license_name": "Creative Commons Attribution 4.0 International", "license_url": "https://creativecommons.org/licenses/by/4.0/", "acknowledgement": null, "contact": null, "pi_names": ["Laura Rogers-Bennett"], "creators": [], "funding": null, "source_accessed": "2026-09-04" }, "links": { "calcofi_org": null, "data_source": "https://library.ucsd.edu/dc/search?q=CalCOFI+Dungeness+crab+megalopae", "workflow": "https://calcofi.io/workflows/ingest_cdfw_dungeness-crab.html", "page": "https://calcofi.io/datasets/cdfw_dungeness-crab/" }, "coverage": { "realm": "bio", "temporal": "1984-05 to 2014-05", "year_min": 1984, "year_max": 2014, "years": [ { "year": 1984, "n_obs": 24, "n_roots": 24 }, { "year": 1988, "n_obs": 10, "n_roots": 10 }, { "year": 1998, "n_obs": 7, "n_roots": 7 }, { "year": 2004, "n_obs": 13, "n_roots": 13 }, { "year": 2005, "n_obs": 15, "n_roots": 15 }, { "year": 2006, "n_obs": 55, "n_roots": 55 }, { "year": 2007, "n_obs": 7, "n_roots": 7 }, { "year": 2008, "n_obs": 189, "n_roots": 102 }, { "year": 2009, "n_obs": 120, "n_roots": 39 }, { "year": 2010, "n_obs": 288, "n_roots": 71 }, { "year": 2011, "n_obs": 164, "n_roots": 41 }, { "year": 2012, "n_obs": 164, "n_roots": 39 }, { "year": 2013, "n_obs": 180, "n_roots": 45 }, { "year": 2014, "n_obs": 220, "n_roots": 55 } ], "spatial": "33.5–51.0°N, 132.2–120.7°W", "bbox": { "lat_min": 33.46, "lat_max": 51.05, "lon_min": -132.25, "lon_max": -120.675 }, "n_obs": 1456, "n_roots": 523, "n_stations": 56, "n_variables": 1, "n_taxa": 3, "depth_min_m": 0, "depth_max_m": 223, "variables": ["abundance"], "life_stages": ["megalopa", "zoea"], "contributes_to": [] }, "tables": ["sample", "obs", "obs_attribute", "sample_measurement", "taxon", "dataset_taxon"], "objects": [ { "table": "obs", "scope": "partition", "shared": false, "path": "ducklake-staging/tables/obs/dataset_key=cdfw_dungeness-crab/1c745a30376e1849871cfa1e/data_0.parquet", "url": "https://storage.googleapis.com/calcofi-db/ducklake-staging/tables/obs/dataset_key=cdfw_dungeness-crab/1c745a30376e1849871cfa1e/data_0.parquet", "bytes": 19852, "sha256": "e171645f282482538a66b03f6b9168528c0066005b54408e3a3ac7a6c31e7e52", "since": "v2026.09.04" } ], "since_version": "v2026.08.25", "distributions": [ { "kind": "download", "url": "https://storage.googleapis.com/calcofi-db/ducklake-staging/tables/obs/dataset_key=cdfw_dungeness-crab/1c745a30376e1849871cfa1e/data_0.parquet", "format": "parquet", "table": "obs", "scope": "partition", "shared": false, "title": "obs (this dataset's rows)", "bytes": 19852, "sha256": "e171645f282482538a66b03f6b9168528c0066005b54408e3a3ac7a6c31e7e52", "since": "v2026.09.04", "status": "current" }, { "kind": "download", "url": "https://storage.calcofi.io/calcofi-files-public/netcdf/cdfw_dungeness-crab/v2026.09.04/cdfw_dungeness-crab.nc", "format": "netcdf", "id": "cdfw_dungeness-crab", "title": "CF netCDF", "bytes": 488626, "sha256": "e002d537da50f9a59315b1f8418c8dece1d604a575fa5aa703aba4db71b58230", "cf_scope": "CF-1.10 where CF applies (coordinates, units, standard names, time). The subsample -> tow -> occurrence hierarchy uses netCDF-4 groups with explicit parent_index links; CF defines no feature type for this nesting.", "release": "v2026.09.04", "generated_utc": "2026-09-04T19:17:31Z", "status": "current" }, { "kind": "service", "url": "https://erddap.calcofi.io/erddap/tabledap/cdfw_dungeness-crab_attribute.html", "format": "erddap", "id": "cdfw_dungeness-crab_attribute", "title": "CDFW Dungeness Crab Megalopae \\u2014 length/stage frequency", "grain": "length/stage frequency", "info_url": "https://erddap.calcofi.io/erddap/info/cdfw_dungeness-crab_attribute/index.html", "status": "current" }, { "kind": "service", "url": "https://erddap.calcofi.io/erddap/tabledap/cdfw_dungeness-crab.html", "format": "erddap", "id": "cdfw_dungeness-crab", "title": "CDFW Dungeness Crab Megalopae \\u2014 observations", "grain": "observations", "info_url": "https://erddap.calcofi.io/erddap/info/cdfw_dungeness-crab/index.html", "status": "current" }, { "kind": "service", "url": "https://erddap.calcofi.io/erddap/tabledap/cdfw_dungeness-crab_sample.html", "format": "erddap", "id": "cdfw_dungeness-crab_sample", "title": "CDFW Dungeness Crab Megalopae \\u2014 sampling events", "grain": "sampling events", "info_url": "https://erddap.calcofi.io/erddap/info/cdfw_dungeness-crab_sample/index.html", "status": "current" }, { "kind": "service", "url": "https://erddap.calcofi.io/erddap/metadata/iso19115/xml/cdfw_dungeness-crab_iso19115.xml", "format": "iso19115", "id": "cdfw_dungeness-crab", "title": "ISO 19115-3 metadata (ERDDAP)", "status": "current" }, { "kind": "notebook", "url": "https://calcofi.io/workflows/ingest_cdfw_dungeness-crab.html", "format": "html", "title": "ingest notebook", "status": "current" }, { "kind": "source", "url": "https://library.ucsd.edu/dc/search?q=CalCOFI+Dungeness+crab+megalopae", "portal": "ucsd-library", "title": "source", "status": "external" } ], "registrations": [ { "portal": "erddap", "status": "published", "url": "https://erddap.calcofi.io/erddap/info/cdfw_dungeness-crab/index.html", "issues": [] }, { "portal": "obis", "status": "n/a", "issues": [] }, { "portal": "edi", "status": "n/a", "issues": [] }, { "portal": "ncei", "status": "n/a", "issues": [] }, { "portal": "caloos", "status": "planned", "issues": [] }, { "portal": "zenodo", "status": "published", "url": "https://doi.org/10.5281/zenodo.22281994", "note": "as part of the integrated database release" } ], "status": { "stage": "ingested", "priority": "nice-to-have", "gh_issue": null, "blockers": "IN THE RELEASE since 2026-08-14 (CC BY 4.0, Q01 answered). 2026-09-03: cut over to EXAMINED SAMPLES ONLY — the core now publishes 526 events (310 sorted time-series subsamples + 216 examined sorting-log tows), down from 2,321; the 1,795 unsorted log rows are dropped from the core entirely (an unexamined archived jar is a fact of the deposit's sorting-log inventory, not a sample of this dataset) and no longer ship as effort-only sample rows. Emits the consolidated core (sample 526 / obs 1456 / obs_attribute 24 / sample_measurement 617 / taxon 17 / dataset_taxon 3) via the generic append_* helpers in-notebook. Coverage now measures 1984-05-17 to 2014-05-03 (was 1949-2014 including unsorted effort). 3 xlsx sources -> 310 examined samples 2008-2014 (24 M. magister megalopae, 15 removal vials / 14 samples) + 216 examined-and-empty sorting-log tows 1984-2009 + 5 verification specimens; station match 306/310 via swfsc_ichthyo. link_data_source is a placeholder UCSD Library RDC search URL pending the deposit's DOI (Q14, new). Q05 open: new sample_type=subsample + cross-dataset parent_sample_key. Q08 (positive-longitude sign error) affects only a dropped unsorted row; deposit README reportedly corrects it — reconcile once the deposit zips are in Drive (Ben, before 2026-09-26).", "updated": "2026-09-03", "questions_open": 9, "questions_dataset": [ { "label": "Q14", "field": "link_data_source", "status": "open" } ] } }, { "dataset_key": "farallon_bird-mammal", "provider": { "key": "farallon", "short": "Farallon Institute", "name": "Farallon Institute", "url": "https://www.faralloninstitute.org", "registered": true }, "dataset": "bird-mammal", "dataset_name": "CalCOFI Bird & Mammal Census", "dataset_name_short": "Seabirds & Marine Mammals", "category": { "name": "Seabirds & Marine Mammals", "realm": "bio", "icon": "cat-birds-mammals", "order": 12, "registered": true }, "color": "#ff8787", "visibility": "public", "description_md": "Bird and mammal observations along CalCOFI (and NMFS, CPR) cruise transects, 1987-present. Transect effort, counts, and species live from NOAA ERDDAP (CAC_FI_SBAS_tr / CAC_FI_SBAS_obs / CAC_FI_SBAS_sp); behavior lookups curated via CCE-LTER DataZoo 255 (PI Bill Sydeman).\n", "keywords": ["EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/VERTEBRATES > BIRDS", "EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/VERTEBRATES > MAMMALS"], "attribution": { "citation_main": null, "citation_others": [], "doi": null, "license": "custom", "license_name": "Custom terms stated by the provider", "license_url": "https://oceanview.pfeg.noaa.gov/CalCOFI/app/resources/docs/Data_Sharing_Agreement_FarallonInstitute.pdf", "acknowledgement": null, "contact": null, "pi_names": ["Bill Sydeman"], "creators": [], "funding": null, "source_accessed": "2026-09-04" }, "links": { "calcofi_org": null, "data_source": "https://oceanview.pfeg.noaa.gov/erddap/tabledap/CAC_FI_SBAS_obs.html", "workflow": "https://calcofi.io/workflows/ingest_farallon_bird-mammal.html", "page": "https://calcofi.io/datasets/farallon_bird-mammal/" }, "coverage": { "realm": "bio", "temporal": "1987-05 to 2022-10", "year_min": 1987, "year_max": 2022, "years": [ { "year": 1987, "n_obs": 1862, "n_roots": 955 }, { "year": 1988, "n_obs": 2880, "n_roots": 1325 }, { "year": 1989, "n_obs": 2694, "n_roots": 1288 }, { "year": 1990, "n_obs": 2799, "n_roots": 1239 }, { "year": 1991, "n_obs": 2603, "n_roots": 1307 }, { "year": 1992, "n_obs": 2939, "n_roots": 1403 }, { "year": 1993, "n_obs": 2619, "n_roots": 1284 }, { "year": 1994, "n_obs": 986, "n_roots": 578 }, { "year": 1995, "n_obs": 2262, "n_roots": 1219 }, { "year": 1996, "n_obs": 1574, "n_roots": 738 }, { "year": 1997, "n_obs": 1748, "n_roots": 842 }, { "year": 1998, "n_obs": 3083, "n_roots": 1480 }, { "year": 1999, "n_obs": 1208, "n_roots": 673 }, { "year": 2000, "n_obs": 1781, "n_roots": 871 }, { "year": 2001, "n_obs": 2720, "n_roots": 1181 }, { "year": 2002, "n_obs": 1731, "n_roots": 971 }, { "year": 2003, "n_obs": 3877, "n_roots": 1962 }, { "year": 2004, "n_obs": 2813, "n_roots": 1421 }, { "year": 2005, "n_obs": 3791, "n_roots": 1687 }, { "year": 2006, "n_obs": 2628, "n_roots": 1291 }, { "year": 2007, "n_obs": 1435, "n_roots": 703 }, { "year": 2008, "n_obs": 954, "n_roots": 534 }, { "year": 2009, "n_obs": 936, "n_roots": 499 }, { "year": 2010, "n_obs": 1242, "n_roots": 697 }, { "year": 2011, "n_obs": 1459, "n_roots": 879 }, { "year": 2012, "n_obs": 1352, "n_roots": 800 }, { "year": 2013, "n_obs": 1277, "n_roots": 639 }, { "year": 2014, "n_obs": 1497, "n_roots": 719 }, { "year": 2015, "n_obs": 1885, "n_roots": 864 }, { "year": 2016, "n_obs": 2189, "n_roots": 1109 }, { "year": 2017, "n_obs": 1898, "n_roots": 938 }, { "year": 2018, "n_obs": 1133, "n_roots": 528 }, { "year": 2019, "n_obs": 1354, "n_roots": 646 }, { "year": 2020, "n_obs": 926, "n_roots": 392 }, { "year": 2022, "n_obs": 1526, "n_roots": 732 } ], "spatial": "29.8–37.8°N, 126.5–117.2°W", "bbox": { "lat_min": 29.77, "lat_max": 37.84, "lon_min": -126.47, 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# source: caloos-sheet row 14, 2026-09-05" } ], "registrations": [ { "portal": "erddap", "status": "published", "url": "https://erddap.calcofi.io/erddap/info/farallon_bird-mammal/index.html", "issues": [] }, { "portal": "obis", "status": "planned", "issue": "https://github.com/CalCOFI/workflows/issues/43", "issues": ["https://github.com/CalCOFI/workflows/issues/43"] }, { "portal": "edi", "status": "planned", "url": "https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-cce.255.3", "issues": [] }, { "portal": "ncei", "status": "n/a", "issues": [] }, { "portal": "caloos", "status": "planned", "url": "https://data.caloos.org/#module-metadata/2458d7c2-af69-4a76-abfb-195fb5aa8f14", "issues": [] }, { "portal": "zenodo", "status": "published", "url": "https://doi.org/10.5281/zenodo.22281994", "note": "as part of the integrated database release" } ], "status": { "stage": "ingested", "priority": "should-complete", "gh_issue": "https://github.com/CalCOFI/workflows/issues/29", "blockers": "transect+obs+species from NOAA ERDDAP CAC_FI_SBAS_* (download-first, 1987-2022; 2021 observations absent upstream, Q11), behavior from DataZoo255; vocabulary staged via append_dataset_taxon() with DataZoo TSNs as ds_source_json (Q10); covers seabird #29 + mammal #30", "updated": "2026-09-03", "questions_open": 11, "questions_dataset": [ { "label": "Q09", "field": "citation_main", "status": "proposed" } ] } }, { "dataset_key": "sio_mesopelagic-fish", "provider": { "key": "sio", "short": "SIO", "name": "Scripps Institution of Oceanography, UC San Diego", "url": "https://scripps.ucsd.edu", "registered": true }, "dataset": "mesopelagic-fish", "dataset_name": "UCSD SIO Mesopelagic Fish", "dataset_name_short": "Mesopelagic Fish", "category": { "name": "Mesopelagic Fish", "realm": "bio", "icon": "cat-fish", "order": 11, "registered": true }, "color": "#5c7cfa", "visibility": "public", "description_md": "Species-resolved mesopelagic fish counts (90 named species + 1 unidentified-fish catch-all) from MOHT (Matsuda-Oozeki-Hu Trawl) micronekton net tows, 7 CalCOFI cruises 2010-2012, all on RV New Horizon (NODC 32NM). Larval-fish counts in the same source file are a separate table, not included here.\n", "keywords": ["EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/VERTEBRATES > FISH", "EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/VERTEBRATES > FISH > RAY-FINNED FISHES"], "attribution": { "citation_main": "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\n", "citation_others": [], "doi": "10.6075/J0BZ64DH", "license": "CC-BY-4.0", "license_name": "Creative Commons Attribution 4.0 International", "license_url": "https://creativecommons.org/licenses/by/4.0/", "acknowledgement": null, "contact": null, "pi_names": ["J. 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Position, time, depth, and gear metadata per tow. Includes the historical grid (1950s-80s inshore, Gulf of California and Baja lines), not just the modern pattern. 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The OBIS text search does not match 'CalCOFI' — address it by this id, never by search." }, { "kind": "archive", "url": "https://ipt-obis.gbif.us/resource?r=calcofi_ichthyo", "portal": "ipt", "id": "calcofi_ichthyo", "title": "CalCOFI Fish Larvae & Egg Tows (OBIS-USA IPT resource)", "status": "current", "observed_utc": "2026-09-05T00:00:00Z", "notes": "the IPT resource behind the OBIS dataset; Ben holds the login; upload is manual, gated on a content change (plan D-8)" }, { "kind": "mirror", "url": "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFIlrvcnt.html", "portal": "erddap-noaa", "id": "erdCalCOFIlrvcnt", "title": "CalCOFI NOAA Fish Larvae Counts", "status": "external", "observed_utc": "2026-09-05T00:00:00Z", "notes": "NOAA CoastWatch ERDDAP; the same SWFSC ichthyoplankton rows served by NOAA (CalOOS module source)" }, { "kind": "mirror", "url": "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFIlrvsiz.html", "portal": "erddap-noaa", "id": "erdCalCOFIlrvsiz", "title": "CalCOFI NOAA Fish Larvae Sizes", "status": "external", "observed_utc": "2026-09-05T00:00:00Z" }, { "kind": "mirror", "url": "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFIlrvstg.html", "portal": "erddap-noaa", "id": "erdCalCOFIlrvstg", "title": "CalCOFI NOAA Fish Larvae Stages", "status": "external", "observed_utc": "2026-09-05T00:00:00Z" }, { "kind": "mirror", "url": "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFIeggcnt.html", "portal": "erddap-noaa", "id": "erdCalCOFIeggcnt", "title": "CalCOFI NOAA Fish Egg Counts", "status": "external", "observed_utc": "2026-09-05T00:00:00Z" }, { "kind": "mirror", "url": "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFIeggstg.html", "portal": "erddap-noaa", "id": "erdCalCOFIeggstg", "title": "CalCOFI NOAA Fish Egg Stages", "status": "external", "observed_utc": "2026-09-05T00:00:00Z" }, { "kind": "mirror", "url": "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFIinvcnt.html", "portal": "erddap-noaa", "id": "erdCalCOFIinvcnt", "title": "CalCOFI NOAA Invertebrate Counts (cephalopods)", "status": "external", "observed_utc": "2026-09-05T00:00:00Z", "notes": "swfsc/invert is folded into swfsc_ichthyo (dataset_status.csv)" }, { "kind": "mirror", "url": "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFIinvsiz.html", "portal": "erddap-noaa", "id": "erdCalCOFIinvsiz", "title": "CalCOFI NOAA Invertebrate Sizes (cephalopods)", "status": "external", "observed_utc": "2026-09-05T00:00:00Z" }, { "kind": "mirror", "url": "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFItows.html", "portal": "erddap-noaa", "id": "erdCalCOFItows", "title": "CalCOFI NOAA Ichthyoplankton Tows", "status": "external", "observed_utc": "2026-09-05T00:00:00Z", "notes": "the tow (effort) table the count tables join to" }, { "kind": "mirror", "url": "https://portal.edirepository.org/nis/mapbrowse?packageid=edi.109.4", "portal": "edi", "id": "edi.109.4", "title": "CALCOFI fish larvae at 66 standard stations, 1966 - ongoing", "status": "external", "observed_utc": "2026-09-05T00:00:00Z", "notes": "SCB MBON's derived package (Thompson, Miller, Kui 2022; doi:10.6073/pasta/23c5576732e5ec3956fe5e86954f4a2b) — a subset of the same source, not the ingest's source; published by MBON, never republished by CalCOFI" }, { "kind": "service", "url": "https://data.caloos.org/#module-metadata/1a1a7812-48f9-4325-8ad0-e51e67e366ba", "portal": "caloos", "id": "1a1a7812-48f9-4325-8ad0-e51e67e366ba", "title": "CalCOFI Fish Eggs & Larvae Counts/Stages from net tows and CUFES (CalOOS module)", "status": "external", "observed_utc": "2026-09-05T00:00:00Z", "notes": "CalOOS catalog module id for the CoastWatch mirror rows; # source: caloos-sheet rows 1,4, 2026-09-05" } ], "registrations": [ { "portal": "erddap", "status": "published", "url": "https://erddap.calcofi.io/erddap/info/swfsc_ichthyo/index.html", "issues": [] }, { "portal": "obis", "status": "published", "url": "https://obis.org/dataset/0e223f55-c826-4513-ae9a-b04cbf2e189c", "issues": [] }, { "portal": "edi", "status": "n/a", "issues": [] }, { "portal": "ncei", "status": "n/a", "issues": [] }, { "portal": "caloos", "status": "planned", "url": "https://data.caloos.org/#module-metadata/1a1a7812-48f9-4325-8ad0-e51e67e366ba", "issues": [] }, { "portal": "zenodo", "status": "published", "url": "https://doi.org/10.5281/zenodo.22281994", "note": "as part of the integrated database release" } ], "status": { "stage": "published", "priority": "must-complete", "gh_issue": null, "blockers": null, "updated": "2026-09-04", "questions_open": 14, "questions_dataset": [ { "label": "Q10", "field": "citation_main", "status": "proposed" }, { "label": "Q11", "field": "license", "status": "proposed" }, { "label": "Q12", "field": "pi_names", "status": "proposed" } ] } } ], "holdings": [ { "dataset_key": "calcofi_prodo", "provider": { "key": "calcofi", "short": "CalCOFI", "name": "California Cooperative Oceanic Fisheries Investigations", "url": "https://calcofi.org", "registered": true }, "dataset": "prodo", "dataset_name": "Measurements from CalCOFI cruises in the California Current System, including log of station information, weather, sea conditions as well as physical, chemical and biological measurements including temperature, salinity, oxygen, density, sigma theta, phosphate, silicate, nitrite, nitrate, ammonia, chlorophyll a, integrated chlorophyll a, primary productivity, and integrated primary production. 1949 - January 2020", "dataset_name_short": null, "category": { "name": "Productivity & Pigments", "realm": "env", "icon": "cat-productivity", "order": 4, "registered": true }, "visibility": "public", "description_md": "CalCOFI PRODO Chlorophyll and Primary Productivity contains chlorophyll a, integrated chlorophyll a, primary productivity, and integrated primary production values drawn from the California Cooperative Oceanic Fisheries Investigations (CalCOFI) hydrographic bottle database, collected during quarterly CalCOFI cruises run by the Scripps Institution of Oceanography (SIO). CalCOFI's hydrographic time series began in 1949 with weather, temperature, salinity, oxygen, and phosphate measurements; nutrient analysis expanded to include silicate, nitrate, and nitrite in 1961, chlorophyll was added in 1973, and carbon-14 primary productivity incubations were added in 1984. The dataset covers primarily the CalCOFI station grid off Southern and Central California, with broader coverage extending farther north, south, and offshore during early cruises, and spans 1949 to 2020. This dataset supports long-term study of phytoplankton biomass and productivity trends in the California Current, for researchers studying multi-decade changes in primary production", "keywords": ["Temperature", "Salinity", "Dissolved Nutrients", "Phytoplankton Biomass and Diversity"], "attribution": { "citation_main": null, "citation_others": [], "doi": "10.6073/pasta/7f8e5d24e9b27ae695295a8ddc0809d1", "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "jwilkinson@ucsd.edu", "pi_names": [], "creators": [ { "name": "James Wilkinson", "organization": "UCSD SIO", "orcid": null, "email": "jwilkinson@ucsd.edu", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-cce&identifier=78&revision=3", "page": "https://calcofi.io/datasets/calcofi_prodo/" }, "distributions": [ { "kind": "source", "url": "https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-cce&identifier=78&revision=3", "portal": "edi", "title": "source", "status": "external" } ], "status": { "stage": "external", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. EDI 78 (PRODO product; abstract says 'drawn from the CalCOFI hydrographic bottle database') -- overlaps calcofi_bottle's chlorophyll/productivity fields; recorded as holding per plan guidance, not a mirror; also #34", "module": "CalCOFI Chlorophyll and Primary Productivity from In Situ 14C Uptake & PRODO, CCE-LTER, SIO, UCSD", "priority_caloos": "EDI", "gh_issue": "https://github.com/CalCOFI/workflows/issues/34" } }, { "dataset_key": "calpoly_whale-edna", "provider": { "key": "calpoly", "short": "Cal Poly", "name": "California Polytechnic State University", "url": "https://www.calpoly.edu", "registered": true }, "dataset": "whale-edna", "dataset_name": "Baleen Whale Density Prediction from Environmental DNA (eDNA)", "dataset_name_short": null, "category": { "name": "Genomics & eDNA", "realm": "bio", "icon": "cat-genomics", "order": 13, "registered": true }, "visibility": "public", "description_md": "Baleen Whale Density Prediction from Environmental DNA (eDNA) contains processed amplicon sequence variant (ASV) abundance tables for three eDNA markers, 16S rRNA, 18S rRNA V4, and 18S rRNA V9, developed by Erin Satterthwaite, Trevor Ruiz, Nastassia Patin, and colleagues to test whether microbial and small zooplankton communities can predict the density of baleen whales in the southern California Current Ecosystem. The dataset covers CalCOFI cruises in the southern California Current Ecosystem and spans 2014 to 2020, combining eDNA data from the NOAA CalCOFI Genomics Program (NCOG) with line-transect distance-sampling density estimates for blue, fin, and humpback whales derived from CalCOFI whale sighting surveys. The data are analyzed using stability selection adapted to sparse partial least squares (sPLS) regression, a statistical method for identifying reliable microbial and zooplankton predictors of whale density within large sequencing datasets. Processed data includes ASV tables with taxonomic annotations, sample metadata, density estimates, and cross-validation partitions. This dataset supports research on eDNA-based indicators of marine mammal distribution and is intended for researchers studying whale ecology and biomonitoring methods in the California Current.", "keywords": ["Zooplankton Biomass and Diversity", "Phytoplankton Biomass and Diversity"], "attribution": { "citation_main": null, "citation_others": [], "doi": null, "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "truiz01@calpoly.edu", "pi_names": [], "creators": [ { "name": "Trevor Ruiz", "organization": "Cal Poly", "orcid": null, "email": "truiz01@calpoly.edu", "role": "lead" } ], "funding": "ONR", "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://doi.org/10.5281/zenodo.19139338", "page": "https://calcofi.io/datasets/calpoly_whale-edna/" }, "distributions": [ { "kind": "source", "url": "https://doi.org/10.5281/zenodo.19139338", "portal": "other", "title": "source", "status": "external" } ], "status": { "stage": "archived", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. Zenodo DOI (baleen whale eDNA) -- new provider calpoly", "module": "NA- one dataset (BUT NOTE: we will likely have more eDNA data that we want part of this catalog in the future)", "priority_caloos": "Other", "gh_issue": null } }, { "dataset_key": "cce-lter_chl-size-fractionated", "provider": { "key": "cce-lter", "short": "CCE-LTER", "name": "California Current Ecosystem Long Term Ecological Research", "url": "https://ccelter.ucsd.edu", "registered": true }, "dataset": "chl-size-fractionated", "dataset_name": "Size fractionation of total Chl a larger and smaller than 8 μm data generated by Mike Mullin of the Marine Life Research Group, aboard CalCOFI (California Cooperative Oceanic Fisheries Investigations) cruises of the coast of California, January 1994 - October 1996", "dataset_name_short": null, "category": { "name": "Productivity & Pigments", "realm": "env", "icon": "cat-productivity", "order": 4, "registered": true }, "visibility": "public", "description_md": "CalCOFI Size-Fractionated Chlorophyll a (>8µm / <8µm) contains depth-integrated chlorophyll a biomass split by cell size (larger and smaller than 8 μm), along with zooplankton displacement volume and nitracline depth, generated by Michael Mullin, Director of the Marine Life Research Group (UC San Diego), from samples collected aboard California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises off the coast of California. The dataset covers twelve quarterly CalCOFI cruises and spans January 1994 to October 1996. At roughly half the stations sampled on each cruise, water was collected at multiple depths using closing bottles on a CTD rosette; chlorophyll from each bottle was retained on a GF/F glass-fiber filter and measured fluorometrically, while an additional combined sample from the shallowest ten bottles (surface to about 100 m) was filtered through an 8 μm membrane filter to isolate the larger size fraction. Total and ≥8 μm chlorophyll were each integrated to 100 m depth, and chlorophyll <8 μm was calculated as the difference between the two. This dataset supports research relating phytoplankton size structure to nitracline depth and zooplankton grazing pressure, for researchers studying controls on phytoplankton community size composition in the California Current.", "keywords": ["Phytoplankton Biomass and Diversity", "CalCOFI Network", "Zooplankton Biomass and Diversity"], "attribution": { "citation_main": null, "citation_others": [], "doi": "10.6073/pasta/02183db3ad041992304d26757f1b25f9", "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": null, "pi_names": [], "creators": [ { "name": "Mike Mullein", "organization": "Marine Life Research Group, IOD/UCSD", "orcid": null, "email": null, "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-cce.249.3", "page": "https://calcofi.io/datasets/cce-lter_chl-size-fractionated/" }, "distributions": [ { "kind": "source", "url": "https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-cce.249.3", "portal": "edi", "title": "source", "status": "external" } ], "status": { "stage": "archived", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. EDI 249 (size-fractionated Chl a) -- new holding; sheet's own DOI matches the newest revision (249.3)", "module": "NA- one dataset", "priority_caloos": null, "gh_issue": null } }, { "dataset_key": "cce-lter_hplc-pigments", "provider": { "key": "cce-lter", "short": "CCE-LTER", "name": "California Current Ecosystem Long Term Ecological Research", "url": "https://ccelter.ucsd.edu", "registered": true }, "dataset": "hplc-pigments", "dataset_name": "High Performance Liquid Chromatography (HPLC) pigment analysis from rosette bottle samples at various depths from CCE LTER process cruises in the California Current System, 2006 to 2017", "dataset_name_short": null, "category": { "name": "Productivity & Pigments", "realm": "env", "icon": "cat-productivity", "order": 4, "registered": true }, "visibility": "public", "description_md": "CalCOFI Phytoplankton Community Taxon-Specific Pigments contains concentrations of chlorophyll and other pigments used to estimate phytoplankton biomass and taxonomic composition, collected during California Current Ecosystem Long-Term Ecological Research (CCE-LTER) Process cruises, periodic research cruises distinct from the routine quarterly California Cooperative Oceanic Fisheries Investigations (CalCOFI) survey. Samples are collected from rosette bottles at three to eight depths in the photic zone at stations within the California Current Ecosystem region, spanning 2006 to 2017. Particulate matter is filtered and frozen at sea, then extracted onshore for High Performance Liquid Chromatography (HPLC) analysis, which measures chlorophyll and carotenoid pigment concentrations. Chlorophyll a concentration serves as a proxy for total phytoplankton biomass, while other taxon-specific pigments are used to determine the contribution of different phytoplankton taxa to that biomass. This dataset supports characterization of phytoplankton community composition and biomass in the California Current, for researchers studying primary producer community structure.", "keywords": ["Phytoplankton Biomass and Diversity"], "attribution": { "citation_main": null, "citation_others": [], "doi": "10.6073/pasta/831e099fb086954d3d73638d33d3dd05", "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "rgoericke@ucsd.edu", "pi_names": [], "creators": [ { "name": "Ralf Goericke", "organization": "UCSD SIO", "orcid": null, "email": "rgoericke@ucsd.edu", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-cce.72.4", "page": "https://calcofi.io/datasets/cce-lter_hplc-pigments/" }, "distributions": [ { "kind": "source", "url": "https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-cce.72.4", "portal": "edi", "title": "source", "status": "external" } ], "status": { "stage": "external", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. EDI 72 (HPLC pigments) is a DIFFERENT variable than calcofi_phytoplankton's visual counts -- not matched", "module": "CalCOFI Phytoplankton community composition (visual microscopy) and taxon-specific pigments (HPLC), CCE-LTER, SIO, UCSD", "priority_caloos": "EDI", "gh_issue": null } }, { "dataset_key": "cce-lter_iron", "provider": { "key": "cce-lter", "short": "CCE-LTER", "name": "California Current Ecosystem Long Term Ecological Research", "url": "https://ccelter.ucsd.edu", "registered": true }, "dataset": "iron", "dataset_name": "Measurements of dissolved inorganic concentrations of nutrient iron and of iron limitation at selected stations and depths from CalCOFI cruises in the California Current System, Nov. 2002 - July 2004 (completed)", "dataset_name_short": null, "category": { "name": "Nutrients & Chemistry", "realm": "env", "icon": "cat-nutrients", "order": 2, "registered": true }, "visibility": "public", "description_md": "CalCOFI Dissolved and Total Iron (Fe) Concentrations contains measurements of dissolved and total iron and results of shipboard iron-addition bioassays, collected during California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises as part of the California Current Ecosystem Long-Term Ecological Research (CCE-LTER) program, with Katherine Barbeau (Scripps Institution of Oceanography (SIO)) as lead contributor, to investigate the potential for phytoplankton iron limitation in the California Current System. The dataset covers coastal transition zone stations of the southern California Current System, a weak-upwelling regime relatively low in nutrients and chlorophyll, and spans November 2002 to July 2004 (completed). Surface (0 m) seawater samples were collected using a pole sampler and analyzed for dissolved iron using an FeLume flow-injection analysis system; a subset of samples also include results from shipboard iron-addition bioassays tracking the chlorophyll a response to added iron (Chla response to Fe+). This dataset supports research on iron limitation and its effects on phytoplankton growth in the California Current, for researchers studying nutrient controls on primary productivity in low-nutrient, low-chlorophyll coastal waters.", "keywords": ["Dissolved Nutrients", "Phytoplankton Biomass and Diversity", "CalCOFI Network"], "attribution": { "citation_main": null, "citation_others": [], "doi": "10.6073/pasta/63c4e57f87861db3acaf80d1dec103e1", "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "kbarbeau@ucsd.edu", "pi_names": [], "creators": [ { "name": "Kathy Barbaeu", "organization": "UCSD SIO", "orcid": null, "email": "kbarbeau@ucsd.edu", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-cce.21.3", "page": "https://calcofi.io/datasets/cce-lter_iron/" }, "distributions": [ { "kind": "source", "url": "https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-cce.21.3", "portal": "edi", "title": "source", "status": "external" } ], "status": { "stage": "archived", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. EDI 21 (dissolved/total iron) -- new holding; sheet's own DOI matches the newest revision (21.3)", "module": "NA- one dataset", "priority_caloos": null, "gh_issue": null } }, { "dataset_key": "cce-lter_poc-pon", "provider": { "key": "cce-lter", "short": "CCE-LTER", "name": "California Current Ecosystem Long Term Ecological Research", "url": "https://ccelter.ucsd.edu", "registered": true }, "dataset": "poc-pon", "dataset_name": "Particulate organic carbon and nitrogen measurements at selected depths in the water column from CalCOFI-CCE Augmented cruises in the California Current System, 2004 - November 2022", "dataset_name_short": null, "category": { "name": "Nutrients & Chemistry", "realm": "env", "icon": "cat-nutrients", "order": 2, "registered": true }, "visibility": "public", "description_md": "CalCOFI Particulate Organic Carbon and Nitrogen (POC/PON) contains concentrations of particulate organic carbon and nitrogen from water column bottle samples collected at multiple depths during California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises since 2004, run by the Scripps Institution of Oceanography (SIO) as part of the California Current Ecosystem Long-Term Ecological Research (CCE-LTER) program. The dataset covers the CalCOFI station grid off Southern and Central California and spans 2004 to ongoing. Samples are filtered at CTD stations, frozen at negative 20 degrees Celsius, then acidified, dried, and analyzed onshore by high-temperature combustion at 1,000 degrees Celsius, which converts organic carbon to carbon dioxide and reduces nitrogen oxides to nitrogen gas, both measured by thermal conductivity. These measurements constrain the mean carbon-to-nitrogen ratio of small particulates and, compared against measured living biomass, estimate the biomass of suspended non-living detritus. This dataset supports study of organic carbon cycling and detrital biomass in the California Current, for researchers studying particulate organic matter dynamics. Its particulate organic carbon values are also used together with CalCOFI's Total Organic Carbon dataset to estimate dissolved organic carbon in open-ocean samples.", "keywords": ["Dissolved Nutrients"], "attribution": { "citation_main": null, "citation_others": [], "doi": "10.6073/pasta/830ff22e75a9de5b493af48330e5fc4c", "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "rgoericke@ucsd.edu", "pi_names": [], "creators": [ { "name": "Ralf Goericke", "organization": "UCSD SIO", "orcid": null, "email": "rgoericke@ucsd.edu", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-cce.54.7", "page": "https://calcofi.io/datasets/cce-lter_poc-pon/" }, "distributions": [ { "kind": "source", "url": "https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-cce.54.7", "portal": "edi", "title": "source", "status": "external" } ], "status": { "stage": "external", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. EDI 54 (POC/PON, CalCOFI-CCE Augmented cruises) -- no ingest", "module": "CalCOFI Particulate and Total Organic Carbon and Nitrogen (POC/PON and TOC), CCE-LTER, SIO, UCSD", "priority_caloos": "EDI", "gh_issue": null } }, { "dataset_key": "cce-lter_poc-pon-cce-region", "provider": { "key": "cce-lter", "short": "CCE-LTER", "name": "California Current Ecosystem Long Term Ecological Research", "url": "https://ccelter.ucsd.edu", "registered": true }, "dataset": "poc-pon-cce-region", "dataset_name": "Particulate organic carbon and nitrogen measurements at selected depths in the water column in the CCE region since 2006 - 2024 (ongoing)", "dataset_name_short": null, "category": { "name": "Nutrients & Chemistry", "realm": "env", "icon": "cat-nutrients", "order": 2, "registered": true }, "visibility": "public", "description_md": "CalCOFI Nitrate Stable Isotope of Nitrogen and Oxygen contains nitrogen and oxygen stable isotope ratios of nitrate, collected from water column bottle samples at multiple depths at CTD stations within the California Current Ecosystem region, during California Current Ecosystem Long-Term Ecological Research (CCE-LTER) Process cruises, periodic research cruises distinct from the routine quarterly California Cooperative Oceanic Fisheries Investigations (CalCOFI) survey. The dataset spans 2006 to ongoing. These isotope ratios, nitrogen-15 and oxygen-18 relative to standard references, are used to trace the origin and cycling of nitrate in seawater. This dataset supports study of nitrogen cycling and nutrient sources in the California Current, for researchers studying ocean biogeochemistry.", "keywords": ["Dissolved Nutrients"], "attribution": { "citation_main": null, "citation_others": [], "doi": "10.6073/pasta/9feb1de01eb3795e7ea39a8b7ba325e6", "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "laluwihare@ucsd.edu", "pi_names": [], "creators": [ { "name": "Lihini Aluwihare", "organization": "UCSD SIO", "orcid": null, "email": "laluwihare@ucsd.edu", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-cce&identifier=104&revision=12", "page": "https://calcofi.io/datasets/cce-lter_poc-pon-cce-region/" }, "distributions": [ { "kind": "source", "url": "https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-cce&identifier=104&revision=12", "portal": "edi", "title": "source", "status": "external" } ], "status": { "stage": "archived", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. CONFLICT: sheet row 26 header/abstract describe nitrate stable isotopes (N15/O18), but EDI knb-lter-cce.104 (the URL given, rev 13 checked 2026-09-05) is titled 'Particulate organic carbon and nitrogen measurements ... in the CCE region since 2006' -- likely a wrong EDI accession in the sheet. Recorded under the verified EDI title; the isotope dataset's real accession is unconfirmed.", "module": "NA- one dataset", "priority_caloos": "EDI", "gh_issue": null } }, { "dataset_key": "cce-lter_primary-production-c14", "provider": { "key": "cce-lter", "short": "CCE-LTER", "name": "California Current Ecosystem Long Term Ecological Research", "url": "https://ccelter.ucsd.edu", "registered": true }, "dataset": "primary-production-c14", "dataset_name": "Primary production estimates from 14C uptake (in situ), determined by the incorporation of inorganic carbon into particulate organic carbon (POC) due to photosynthesis at selected light levels from CCE LTER process cruises in the California Current System, 2006 - 2021 (ongoing)", "dataset_name_short": null, "category": { "name": "Productivity & Pigments", "realm": "env", "icon": "cat-productivity", "order": 4, "registered": true }, "visibility": "public", "description_md": "CalCOFI Primary Production from 14C Uptake (in Situ) contains measurements of phytoplankton photosynthetic production rates from seawater samples collected each day near midday during California Current Ecosystem Long-Term Ecological Research (CCE-LTER) Process cruises, within the California Current Ecosystem region. The dataset spans 2006 to 2021. Water is collected via Niskin bottles from the CTD rosette at depths matching specific light levels, determined from Secchi disk measurements of light penetration, then incubated on deck under matching simulated light and dosed with radioactive carbon-14. The amount of carbon-14 taken up by phytoplankton during photosynthesis, after filtering, estimates the rate of primary production, reported in micrograms of carbon per liter per day, at each light level sampled within the euphotic zone. This dataset supports study of phytoplankton productivity and carbon fixation rates in the California Current, for researchers studying primary production and ecosystem energy flow.", "keywords": ["Phytoplankton Biomass and Diversity"], "attribution": { "citation_main": null, "citation_others": [], "doi": "10.6073/pasta/0b954fc2d13835a58bdbf17aa5119d34", "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "rgoericke@ucsd.edu", "pi_names": [], "creators": [ { "name": "Ralf Goericke", "organization": "UCSD SIO", "orcid": null, "email": "rgoericke@ucsd.edu", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-cce.71.4", "page": "https://calcofi.io/datasets/cce-lter_primary-production-c14/" }, "distributions": [ { "kind": "source", "url": "https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-cce.71.4", "portal": "edi", "title": "source", "status": "external" } ], "status": { "stage": "external", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. EDI 71 (primary production, C14 uptake) -- overlaps dataset_status.csv calcofi/prodo #34", "module": "CalCOFI Chlorophyll and Primary Productivity from In Situ 14C Uptake & PRODO, CCE-LTER, SIO, UCSD", "priority_caloos": "CalCOFI website", "gh_issue": "https://github.com/CalCOFI/workflows/issues/34" } }, { "dataset_key": "cce-lter_toc", "provider": { "key": "cce-lter", "short": "CCE-LTER", "name": "California Current Ecosystem Long Term Ecological Research", "url": "https://ccelter.ucsd.edu", "registered": true }, "dataset": "toc", "dataset_name": "Total dissolved organic carbon measurements at standard depths in the water column from nine CalCOFI cruises, 2008-2017", "dataset_name_short": null, "category": { "name": "Nutrients & Chemistry", "realm": "env", "icon": "cat-nutrients", "order": 2, "registered": true }, "visibility": "public", "description_md": "CalCOFI Total Organic Carbon (TOC) contains total organic carbon concentrations, combining both dissolved and particulate organic carbon, from water column bottle samples collected at multiple depths during California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises at CTD stations, run by the Scripps Institution of Oceanography (SIO) as part of the California Current Ecosystem Long-Term Ecological Research (CCE-LTER) program. The dataset covers the CalCOFI station grid off Southern and Central California and spans 2008 to 2017. TOC is measured onshore in the lab and reported as micromoles of carbon per liter of seawater. In open ocean waters, particulate organic carbon can be subtracted from TOC to estimate dissolved organic carbon, since particles there are typically small and evenly distributed. In coastal waters and at stations with high chlorophyll, particles are larger and unevenly distributed, so this subtraction does not reliably estimate dissolved organic carbon, and samples from the California Current Ecosystem are reported as TOC rather than converted. This dataset supports study of organic carbon cycling in coastal and open ocean waters of the California Current, for researchers studying carbon dynamics in the California Current ecosystem. It complements CalCOFI's Particulate Organic Carbon and Nitrogen (POC/PON) dataset, whose values are used together with TOC to estimate dissolved organic carbon in open-ocean samples.", "keywords": ["Dissolved Nutrients"], "attribution": { "citation_main": null, "citation_others": [], "doi": "10.6073/pasta/ba2ce7e921448a75372109d9f2f5cab2", "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "laluwihare@ucsd.edu", "pi_names": [], "creators": [ { "name": "Lihini Aluwihare", "organization": "UCSD SIO", "orcid": null, "email": "laluwihare@ucsd.edu", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-cce&identifier=253&revision=3", "page": "https://calcofi.io/datasets/cce-lter_toc/" }, "distributions": [ { "kind": "source", "url": "https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-cce&identifier=253&revision=3", "portal": "edi", "title": "source", "status": "external" } ], "status": { "stage": "external", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. EDI 253 (TOC) -- no ingest", "module": "CalCOFI Particulate and Total Organic Carbon and Nitrogen (POC/PON and TOC), CCE-LTER, SIO, UCSD", "priority_caloos": "EDI", "gh_issue": null } }, { "dataset_key": "jcvi_ncog-metabarcoding", "provider": { "key": "jcvi", "short": "JCVI", "name": "J. Craig Venter Institute", "url": "https://www.jcvi.org", "registered": true }, "dataset": "ncog-metabarcoding", "dataset_name": "CalCOFI Microbial/Plankton Community Genomics (16S and 18S rDNA) NCOG- JCVI & SIO, UCSD", "dataset_name_short": null, "category": { "name": "Genomics & eDNA", "realm": "bio", "icon": "cat-genomics", "order": 13, "registered": true }, "visibility": "public", "description_md": "CalCOFI Microbial/Plankton Community Genomics (16S and 18S rDNA) contains ribosomal RNA (rRNA) gene metabarcoding sequence data, collected as part of the NOAA CalCOFI Genomics Program (NCOG) to characterize microbial and plankton community composition in the California Current. The dataset covers CalCOFI and California Current Ecosystem Long-Term Ecological Research (CCE-LTER) stations off Southern and Central California and spans 2014 to 2019, archived across two NCBI BioProject deposits (PRJNA555783 for 2014-2016 and PRJNA665326 for 2017-2019, which also includes some 2014-2016 samples and extends metatranscriptomics data through 2020). Whole water samples were filtered onto 0.2 micrometer filters to capture DNA and RNA at four depths, 10 meters, the subsurface chlorophyll maximum layer, 170 meters, and 515 meters, then sequenced using 16S V4 metabarcoding to identify bacteria and archaea, and 18S V4 and V9 metabarcoding to identify eukaryotic plankton such as protists and small zooplankton. The same archived deposits also include total mRNA sequencing (metatranscriptomics) data from these samples. This dataset supports research identifying amplicon sequence variants (ASVs), a method for distinguishing microbial and plankton taxa at high resolution, and characterizing community structure and diversity, and is intended for researchers studying plankton and microbial ecology in the California Current.", "keywords": ["Phytoplankton Biomass and Diversity"], "attribution": { "citation_main": null, "citation_others": [], "doi": null, "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "aallen@ucsd.edu", "pi_names": [], "creators": [ { "name": "Andy Allen", "organization": "J. Craig Venter Institute (JCVI)", "orcid": null, "email": "aallen@ucsd.edu", "role": "lead" } ], "funding": "NSF (OCE-1637632), NOAA (NA15OAR4320071), Gordon and Betty Moore Foundation (GBMF3828)", "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://www.ncbi.nlm.nih.gov/bioproject/555783", "page": "https://calcofi.io/datasets/jcvi_ncog-metabarcoding/" }, "distributions": [ { "kind": "source", "url": "https://www.ncbi.nlm.nih.gov/bioproject/555783", "portal": "ncbi", "title": "source", "status": "external" } ], "status": { "stage": "external", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. NCBI BioProjects 555783/665326 -- new provider jcvi", "module": "NA- one dataset (BUT NOTE: we will likely have more eDNA data that we want part of this catalog in the future)", "priority_caloos": "NCBI", "gh_issue": null } }, { "dataset_key": "sccoos_ifcb-ctd", "provider": { "key": "sccoos", "short": "SCCOOS", "name": "Southern California Coastal Ocean Observing System", "url": "https://sccoos.org", "registered": true }, "dataset": "ifcb-ctd", "dataset_name": "CalCOFI Imaging FlowCytobot (IFCB) Images of Chloroplast-Containing Plankton from CTD - SIO, UCSD", "dataset_name_short": null, "category": { "name": "Phytoplankton", "realm": "bio", "icon": "cat-phytoplankton", "order": 6, "registered": true }, "visibility": "public", "description_md": "CalCOFI Imaging FlowCytobot (IFCB) Images of Chloroplast-Containing Plankton from CTD contains high-resolution digital images of chloroplast-containing plankton and other suspended particles, collected during California Cooperative Oceanic Fisheries Investigations (CalCOFI) CTD casts to characterize fine-scale plankton community composition. The dataset covers the southern California Current and spans 2022 to ongoing, since the Imaging FlowCytobot (IFCB) was first deployed on CalCOFI cruises. Discrete water samples are collected from 10 meters and the chlorophyll maximum depth during CTD casts and imaged using the IFCB, an automated flow cytometer that combines flow cytometry and video technology to photograph individual suspended particles. Images are processed to estimate particle volume and identity, along with geolocation, sampling conditions, and instrument metadata, allowing estimates of plankton abundance, biovolume, and carbon content. This dataset supports research on fine-scale plankton community composition and spatial and temporal variability, and is intended for researchers studying phytoplankton ecology in the California Current.", "keywords": ["Phytoplankton Biomass and Diversity", "CalCOFI Network"], "attribution": { "citation_main": null, "citation_others": [], "doi": null, "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "aallen@ucsd.edu", "pi_names": [], "creators": [ { "name": "Andy Allen", "organization": "JCVI, UCSD SIO", "orcid": null, "email": "aallen@ucsd.edu", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://ifcb.caloos.org/timeline?dataset=calcofi-cruises-ctd", "page": "https://calcofi.io/datasets/sccoos_ifcb-ctd/" }, "distributions": [ { "kind": "source", "url": "https://ifcb.caloos.org/timeline?dataset=calcofi-cruises-ctd", "portal": "caloos", "title": "source", "status": "external" } ], "status": { "stage": "external", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. ifcb.caloos.org CTD timeline -- provider sccoos (CalOOS/SCCOOS-hosted IFCB)", "module": "CalCOFI Imaging FlowCytobot (IFCB) Images of Chloroplast-Containing Plankton from CTD & Underway data, CCE-LTER, SIO, UCSD", "priority_caloos": "CalOOS", "gh_issue": null } }, { "dataset_key": "sccoos_ifcb-underway", "provider": { "key": "sccoos", "short": "SCCOOS", "name": "Southern California Coastal Ocean Observing System", "url": "https://sccoos.org", "registered": true }, "dataset": "ifcb-underway", "dataset_name": "CalCOFI Imaging FlowCytobot (IFCB) Images of Chloroplast-Containing Plankton from Underway data - SIO, UCSD", "dataset_name_short": null, "category": { "name": "Phytoplankton", "realm": "bio", "icon": "cat-phytoplankton", "order": 6, "registered": true }, "visibility": "public", "description_md": "CalCOFI Imaging FlowCytobot (IFCB) Images of Chloroplast-Containing Plankton from Underway data contains high-resolution digital images of chloroplast-containing plankton and other suspended particles, collected continuously during California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises to characterize fine-scale plankton community composition. The dataset covers the southern California Current and spans 2022 to ongoing, since the Imaging FlowCytobot (IFCB) was first deployed on CalCOFI cruises. Seawater is drawn continuously through the ship's underway system and imaged by the IFCB in small increments approximately every 20 to 25 minutes, using an automated flow cytometer that combines flow cytometry and video technology to photograph individual suspended particles. Images are processed to estimate particle volume and identity, along with geolocation, sampling conditions, and instrument metadata, allowing estimates of plankton abundance, biovolume, and carbon content. This dataset supports research on fine-scale plankton community composition and spatial and temporal variability, and is intended for researchers studying phytoplankton ecology in the California Current.", "keywords": [], "attribution": { "citation_main": null, "citation_others": [], "doi": null, "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "aallen@ucsd.edu", "pi_names": [], "creators": [ { "name": "Andy Allen", "organization": "JCVI, UCSD SIO", "orcid": null, "email": "aallen@ucsd.edu", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://ifcb.caloos.org/timeline?dataset=calcofi-cruises-underway", "page": "https://calcofi.io/datasets/sccoos_ifcb-underway/" }, "distributions": [ { "kind": "source", "url": "https://ifcb.caloos.org/timeline?dataset=calcofi-cruises-underway", "portal": "caloos", "title": "source", "status": "external" } ], "status": { "stage": "external", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. ifcb.caloos.org underway timeline", "module": "CalCOFI Imaging FlowCytobot (IFCB) Images of Chloroplast-Containing Plankton from CTD & Underway data, CCE-LTER, SIO, UCSD", "priority_caloos": "CalOOS", "gh_issue": null } }, { "dataset_key": "sio_cetacean-sightings", "provider": { "key": "sio", "short": "SIO", "name": "Scripps Institution of Oceanography, UC San Diego", "url": "https://scripps.ucsd.edu", "registered": true }, "dataset": "cetacean-sightings", "dataset_name": "Index of visual monitoring, location, species behavior, and identification of cetaceans from CalCOFI cruises in the California Current System, 2005-2015 (ongoing)", "dataset_name_short": null, "category": { "name": "Seabirds & Marine Mammals", "realm": "bio", "icon": "cat-birds-mammals", "order": 12, "registered": true }, "visibility": "public", "description_md": "CalCOFI Underway Marine Mammal Sighting Surveys contains visual sighting records of cetaceans (whales and dolphins) collected during California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises, run by the Scripps Institution of Oceanography (SIO), to understand cetacean ecology and habitat use. The dataset covers the CalCOFI station grid off Southern and Central California, recorded while the ship transits between stations, and spans 2004 to 2015, with cruises conducted quarterly. Trained observers watch for cetaceans during daylight hours using standard line-transect distance-sampling methods (Burnham et al. 1980; Buckland et al. 1993; Barlow 1995), recording each sighting's location and distance from the ship's track. Surveys are conducted during favorable weather, with calm seas (Beaufort state 5 or below) and visibility beyond 1 nautical mile. This dataset supports study of cetacean distribution and habitat use relative to oceanographic conditions, for researchers studying marine mammal ecology in the California Current.", "keywords": ["\"Marine Turtles", "Birds", "and Mammals\""], "attribution": { "citation_main": null, "citation_others": [], "doi": "10.6073/pasta/9ee6ca9b4a316708ca3d17ddc92debfb", "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "jahildebrand@ucsd.edu", "pi_names": [], "creators": [ { "name": "John Hildebrand & Simone Baumann Pickering", "organization": "UCSD SIO", "orcid": null, "email": "jahildebrand@ucsd.edu", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://oceaninformatics.ucsd.edu/datazoo/catalogs/ccelter/datasets/284", "page": "https://calcofi.io/datasets/sio_cetacean-sightings/" }, "distributions": [ { "kind": "source", "url": "https://oceaninformatics.ucsd.edu/datazoo/catalogs/ccelter/datasets/284", "portal": "datazoo", "title": "source", "status": "external" } ], "status": { "stage": "external", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. EDI 262 (Hildebrand cetacean visual monitoring) is NOT farallon_bird-mammal's EDI 255 (Sydeman bird/mammal census) -- a different package/PI", "module": "CalCOFI Underway Marine Mammal Sighting Surveys - SIO, UCSD", "priority_caloos": "EDI", "gh_issue": null } }, { "dataset_key": "stanford_hopkins-phytoplankton", "provider": { "key": "stanford", "short": "Stanford Hopkins MS", "name": "Hopkins Marine Station, Stanford University", "url": "https://hopkinsmarinestation.stanford.edu", "registered": true }, "dataset": "hopkins-phytoplankton", "dataset_name": "Stanford Hopkins Marine Station CalCOFI Phytoplankton Data", "dataset_name_short": null, "category": { "name": "Phytoplankton", "realm": "bio", "icon": "cat-phytoplankton", "order": 6, "registered": true }, "visibility": "public", "description_md": "Stanford Hopkins Marine Station CalCOFI Phytoplankton Data contains transcribed records of phytoplankton composition, collected by the Hopkins Marine Station of Stanford University as part of the California Cooperative Oceanic Fisheries Investigations (CalCOFI) program to help understand the environmental conditions surrounding the collapse of the California sardine fishery. The dataset covers Monterey Bay, California, and spans 1954 to 1968, a subset of Hopkins Marine Station's broader weekly CalCOFI sampling program that ran from March 1951 through June 1974. Data were collected through weekly field sampling and later transcribed from the original raw and aggregated records held at the Hopkins Marine Station library. This dataset supports historical research on phytoplankton community composition in Monterey Bay, extending oceanographic observations in the Northeast Pacific decades into the past, and is intended for researchers studying long-term or historical trends in phytoplankton populations and California Current oceanography. This dataset covers only a subset of the full 1951 to 1974 Hopkins Marine Station sampling period; Moss Landing Marine Laboratories took over the Monterey Bay sampling program in July 1974, continuing similar sampling until it appears to have ended in 1979.", "keywords": ["Phytoplankton Biomass and Diversity", "CalCOFI Network"], "attribution": { "citation_main": null, "citation_others": [], "doi": null, "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "thalassa@stanford.edu", "pi_names": [], "creators": [ { "name": "Amanda Whitmire", "organization": "Hopkins Marine Station, Stanford University", "orcid": null, "email": "thalassa@stanford.edu", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://searchworks.stanford.edu/view/pz376rp0413", "page": "https://calcofi.io/datasets/stanford_hopkins-phytoplankton/" }, "distributions": [ { "kind": "source", "url": "https://searchworks.stanford.edu/view/pz376rp0413", "portal": "other", "title": "source", "status": "external" } ], "status": { "stage": "archived", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. searchworks.stanford.edu/view/pz376rp0413 -- a specific catalog record", "module": "CalCOFI Zooplankton, Phytoplankton and Supplemental Data from Monterey Bay (1955–1963), Stanford Hopkins Marine Station", "priority_caloos": "Other", "gh_issue": null } }, { "dataset_key": "stanford_hopkins-supplemental", "provider": { "key": "stanford", "short": "Stanford Hopkins MS", "name": "Hopkins Marine Station, Stanford University", "url": "https://hopkinsmarinestation.stanford.edu", "registered": true }, "dataset": "hopkins-supplemental", "dataset_name": "CalCOFI Supplemental Data from Monterey Bay (1955-1963) - Stanford Hopkins Marine Station", "dataset_name_short": null, "category": { "name": "Physical Oceanography", "realm": "env", "icon": "cat-physical", "order": 1, "registered": true }, "visibility": "public", "description_md": "CalCOFI Supplemental Data from Monterey Bay contains additional hydrographic, meteorological, and biological observations collected by the Hopkins Marine Station of Stanford University as part of the California Cooperative Oceanic Fisheries Investigations (CalCOFI) program, including temperature, salinity, dissolved oxygen, phosphate, silicate, meteorological conditions, and fish and marine mammal counts. The dataset covers Monterey Bay, California, as part of Hopkins Marine Station's weekly CalCOFI sampling program that ran from March 1951 through June 1974. The underlying records exist primarily as digitized images and PDF scans of the original field notebooks and reports, housed in the Stanford Digital Repository, with extraction into a structured, actionable dataset still in progress as of the most recent public update. This dataset supports historical research on oceanographic and ecological conditions in Monterey Bay and is intended for researchers studying long-term environmental change in the California Current.", "keywords": [], "attribution": { "citation_main": null, "citation_others": [], "doi": null, "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "thalassa@stanford.edu", "pi_names": [], "creators": [ { "name": "Amanda Whitmire", "organization": "Hopkins Marine Station, Stanford University", "orcid": null, "email": "thalassa@stanford.edu", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://searchworks.stanford.edu/catalog?utf8=%E2%9C%93&search_field=search&q=calcofi", "page": "https://calcofi.io/datasets/stanford_hopkins-supplemental/" }, "distributions": [ { "kind": "source", "url": "https://searchworks.stanford.edu/catalog?utf8=%E2%9C%93&search_field=search&q=calcofi", "portal": "other", "title": "source", "status": "external" } ], "status": { "stage": "archived", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. abstract describes real content (hydrographic/met/bio field-notebook scans) distinct from 33/35, not a duplicate; access URL is a generic SearchWorks query pending a specific record", "module": "CalCOFI Zooplankton, Phytoplankton and Supplemental Data from Monterey Bay (1955–1963), Stanford Hopkins Marine Station", "priority_caloos": "Other", "gh_issue": null } }, { "dataset_key": "stanford_hopkins-zooplankton", "provider": { "key": "stanford", "short": "Stanford Hopkins MS", "name": "Hopkins Marine Station, Stanford University", "url": "https://hopkinsmarinestation.stanford.edu", "registered": true }, "dataset": "hopkins-zooplankton", "dataset_name": "CalCOFI Zooplankton Data from Monterey Bay (1955-1963) - Stanford Hopkins Marine Station", "dataset_name_short": null, "category": { "name": "Zooplankton", "realm": "bio", "icon": "cat-zooplankton", "order": 8, "registered": true }, "visibility": "public", "description_md": "CalCOFI Zooplankton Data from Monterey Bay (1955-1963) contains transcribed records of zooplankton composition and seasonal distribution, collected by the Hopkins Marine Station of Stanford University as part of the California Cooperative Oceanic Fisheries Investigations (CalCOFI) program to help understand the environmental conditions surrounding the collapse of the California sardine fishery. The dataset covers Monterey Bay, California, and spans 1955 to 1963, a subset of Hopkins Marine Station's broader weekly CalCOFI sampling program that ran from March 1951 through June 1974. Data were collected through weekly field sampling and later transcribed from the original paper records through a crowdsourcing campaign. This dataset supports historical research on zooplankton community structure and seasonal patterns in Monterey Bay, extending oceanographic observations in the Northeast Pacific decades into the past, and is intended for researchers studying long-term or historical trends in zooplankton populations. This dataset covers only a subset of the full 1951 to 1974 Hopkins Marine Station sampling period; a separate program at Moss Landing Marine Laboratories continued similar sampling from 1974 to 1979.", "keywords": ["Zooplankton Biomass and Diversity"], "attribution": { "citation_main": null, "citation_others": [], "doi": null, "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "thalassa@stanford.edu", "pi_names": [], "creators": [ { "name": "Amanda Whitmire", "organization": "Hopkins Marine Station, Stanford University", "orcid": null, "email": "thalassa@stanford.edu", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://doi.org/10.25740/nt620vn7810", "page": "https://calcofi.io/datasets/stanford_hopkins-zooplankton/" }, "distributions": [ { "kind": "source", "url": "https://doi.org/10.25740/nt620vn7810", "portal": "other", "title": "source", "status": "external" } ], "status": { "stage": "archived", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. Stanford Digital Repository DOI 10.25740/nt620vn7810 -- new provider stanford", "module": "CalCOFI Zooplankton, Phytoplankton and Supplemental Data from Monterey Bay (1955–1963), Stanford Hopkins Marine Station", "priority_caloos": "Other", "gh_issue": null } }, { "dataset_key": "swfsc_ctd-noaa", "provider": { "key": "swfsc", "short": "NOAA SWFSC", "name": "NOAA Southwest Fisheries Science Center", "url": "https://www.fisheries.noaa.gov/about/southwest-fisheries-science-center", "registered": true }, "dataset": "ctd-noaa", "dataset_name": "CalCOFI Additional CTD Hydrographic Cast Data-NOAA SWFSC", "dataset_name_short": null, "category": { "name": "Physical Oceanography", "realm": "env", "icon": "cat-physical", "order": 1, "registered": true }, "visibility": "public", "description_md": "CalCOFI Additional CTD Hydrographic Cast Data contains temperature, salinity, and dissolved oxygen measurements from CTD (conductivity-temperature-depth) casts taken during California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises and related NOAA cruises. The dataset covers primarily the CalCOFI station grid off Southern and Central California, with related NOAA cruises extending north into the Pacific Northwest and offshore, and spans 2002 to 2014. A CTD instrument is lowered through the water column at each station, recording temperature, salinity, dissolved oxygen concentration and saturation, and depth to about 1,000 meters. Most oxygen and salinity values here have not been calibrated against water samples, so users needing calibrated hydrographic data should use the SIO CalCOFI CTD cast and bottle datasets instead, which are corrected using bottle sample comparisons. This dataset is best used as a supplementary record of additional NOAA CTD casts outside the primary SIO hydrographic time series.", "keywords": ["Temperature", "Salinity", "Dissolved Oxygen", "CalCOFI Network"], "attribution": { "citation_main": null, "citation_others": [], "doi": null, "license": null, "license_name": null, "license_url": null, "acknowledgement": null, "contact": "ed.weber@noaa.gov", "pi_names": [], "creators": [ { "name": "Ed Weber", "organization": "NOAA SWFSC", "orcid": null, "email": "ed.weber@noaa.gov", "role": "lead" } ], "funding": null, "source_accessed": null }, "links": { "calcofi_org": null, "data_source": "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFINOAAhydros.html", "page": "https://calcofi.io/datasets/swfsc_ctd-noaa/" }, "distributions": [ { "kind": "source", "url": "https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFINOAAhydros.html", "portal": "erddap-noaa", "title": "source", "status": "external" } ], "status": { "stage": "external", "priority": null, "owner": null, "next_step": "confirm dataset scope, license and DOI with the provider; no ingest planned yet. erdCalCOFINOAAhydros is NOT a mirror of calcofi_ctd-cast (uncalibrated, per its own abstract) -- a holding candidate", "module": "CalCOFI Additional CTD Hydrographic Cast Data-NOAA SWFSC", "priority_caloos": "ERDDAP", "gh_issue": null } } ], "reference": [ { "key": "cruise", "kind": "table", "name": "Cruise", "description_md": "unique by ship and year-month", "rows": 842, "url": "https://storage.googleapis.com/calcofi-db/ducklake-staging/tables/cruise/829f8b61e2af101e53a0c484/cruise.parquet", "schema_url": "https://calcofi.io/db-schema/#cruise" }, { "key": "ship", "kind": "table", "name": "Ship", "description_md": "unique ship with many cruises", "rows": 49, "url": "https://storage.googleapis.com/calcofi-db/ducklake-staging/tables/ship/9a88861433301d3665cb140d/ship.parquet", "schema_url": "https://calcofi.io/db-schema/#ship" }, { "key": "grid", "kind": "table", "name": "Grid", "description_md": "CalCOFI survey grid polygons with standard and historical station patterns", "rows": 218, "url": "https://storage.googleapis.com/calcofi-db/ducklake-staging/tables/grid/2b546ac2ee0a112afbf96bd5/grid.parquet", "schema_url": "https://calcofi.io/db-schema/#grid" }, { "key": "spatial", "kind": "table", "name": "Spatial Layers", "description_md": "Geometries for ancillary spatial layers (CA jurisdictions NOAA boundaries marine protected areas etc.) keyed by spatial_key. 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180, 71.7881], "source": "noaa_maritime_boundaries", "url": "https://storage.googleapis.com/calcofi-files-public/_spatial/noaa_maritime_boundaries.pmtiles", "built": "2026-08-24" }, { "key": "noaa_maritime_eez", "kind": "layer", "name": "200NM EEZ", "group": "Maritime Zones", "description_md": "US 200 nautical mile exclusive economic zone", "attribution": "NOAA Office of Coast Survey", "n_features": 67, "bbox": [-180, -17.555, 180, 74.7088], "source": "noaa_maritime_boundaries", "url": "https://storage.googleapis.com/calcofi-files-public/_spatial/noaa_maritime_boundaries.pmtiles", "built": "2026-08-24" }, { "key": "ca_maritime_boundaries", "kind": "layer", "name": "CA State Waters (3NM)", "group": "Maritime Zones", "description_md": "California 3 nautical mile state waters boundary", "attribution": "CA Dept of Fish and Wildlife", "n_features": 1, "bbox": [-124.475, 32.5001, -117.097, 41.9999], "source": "ca_maritime_boundaries", "url": 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