The California Cooperative Oceanic Fisheries Investigations (CalCOFI)

In 1951, the Hopkins Marine Station of Stanford University became involved in the California Cooperative Oceanic Fisheries Investigations (CalCOFI) program to collect oceanographic data in and near Monterey Bay. Hopkins staff conducted weekly sampling (more or less) continuously from March 1951 through June 1974. Moss Landing Marine Laboratories (MLML) took over the Monterey Bay sampling program in July 1974, and it appears to have ended in 1979. The aim of the initial program was to conduct joint fisheries-oceanographic cruises that would help researchers understand what contributed to the crash of the California sardine fishery. The Hopkins Marine Station CalCOFI dataset is an extremely important contribution to early oceanographic research in the Northeast Pacific Ocean, and extends our observations in this area decades into the past. The raw and aggregated data for most of these cruises currently resides in the library at the Hopkins Marine Station. This portion of the dataset is a transcription of the zooplankton data that was collected from 1955 to 1963 (a subset of the full HMS CalCOFI program). These spreadsheets are the output of a crowdsourcing campaign on the 'From the Page' platform. We thank 58 contributors for transcribing over 1500 pages! See the dataset README file for detailed information about the data.

Fish larvae counts and standardized counts for larvae captured in CalCOFI icthyoplankton nets (primarily vertical [Calvet or Pairovet], oblique [bongo or ring nets], and surface tows [Manta nets]). Surface tows are normally standardized to count per 1,000 m3 strained. Oblique tows are normally standardized to count per 10 m2 of surface sampled. This table includes all tows by species, even if zero larvae were captured for the species, i.e., negative tows. The "Larvae Counts Positive Tows" table includes only tows where one or more larvae were captured for the species selected by the user.

SIO Hydrographic data. See https://wp.calcofi.org/wp/sampling-info/methods/bottle-sampling-methods/

Context

The CalCOFI data set represents the longest (1949-present) and most complete (more than 50,000 sampling stations) time series of oceanographic and larval fish data in the world. It includes abundance data on the larvae of over 250 species of fish; larval length frequency data and egg abundance data on key commercial species; and oceanographic and plankton data. The physical, chemical, and biological data collected at regular time and space intervals quickly became valuable for documenting climatic cycles in the California Current and a range of biological responses to them. CalCOFI research drew world attention to the biological response to the dramatic Pacific-warming event in 1957-58 and introduced the term “El Niño” into the scientific literature.

The California Cooperative Oceanic Fisheries Investigations (CalCOFI) are a unique partnership of the California Department of Fish & Wildlife, NOAA Fisheries Service and Scripps Institution of Oceanography. The organization was formed in 1949 to study the ecological aspects of the sardine population collapse off California. Today our focus has shifted to the study of the marine environment off the coast of California, the management of its living resources, and monitoring the indicators of El Nino and climate change. CalCOFI conducts quarterly cruises off southern & central California, collecting a suite of hydrographic and biological data on station and underway. Data collected at depths down to 500 m include: temperature, salinity, oxygen, phosphate, silicate, nitrate and nitrite, chlorophyll, transmissometer, PAR, C14 primary productivity, phytoplankton biodiversity, zooplankton biomass, and zooplankton biodiversity.

Content

Each table has several dozen columns. Please see this page for the table details.

This collection includes data collected from multiple platforms in the coastal waters of California over many years, as part of the California Cooperative Fisheries Investigation (CalCOFI) project. CalCOFI has been observing the California Current since 1949 to understand and predict the effects of climate change on marine ecosystems.

This collection includes physical measurements and observations of temperature, conductivity, pressure, salinity, density, sound velocity, sigma-t, depth, humidity, photosynthetic active radiation (PAR), light transmission, turbidity, solids, water color, tide, current, sea, swell, wave, weather, wind, cloud, chemical measurements and observations of alkalinity, ammonia (NH3), ammonium (NH4), nitrate, nitrite, nitrogen, carbon, oxygen, pH, phosphate, phosphorus, polychlorinated biphenyls, silicate, urea, biological measurements and observations of chlorophyll, productivity, fluorescence, phaeophytin, phaeopigment, phytoplankton, zooplankton, as well as fishery surveys and other data.

Dataset

This dataset was created by Gmastersixtyfo

Contents

The data included in this dataset are bird and mammal observations from aboard research cruises. There are six tables of data: a transect log and observation log pairing for each of the three types of cruises. California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises are conducted quarterly off the coast of southern and central California. National Marine Fisheries (NMFS) cruises are a part of the Rockfish Recruitment Survey off the coast of southern and central California. Data were also collected aboard North Pacific Continuous Plankton Recorder (NPCPR) cruises from June 2002 through May 2006. Observations of birds and mammals include both number and behavior in addition to temporal and spatial information recorded along the cruise transect. Data are collected in order to research the interdependent aspects of the marine environment, including the effects of natural and human based climate change, and the broad implications and influences of ocean currents, weather patterns, fishing practices and coastal development on marine food webs and ecosystem processes.

Species and behavior definitions for data codes are available in the "Supplemental Documents" section.

IFCB CalCOFI

## Overview

IFCB CalCOFI is a dataset for object detection tasks - it contains Phytoplanktons annotations for 4,095 images.

## Getting Started

You can download this dataset for use within your own projects, or fork it into a workspace on Roboflow to create your own model.

  ## License

  This dataset is available under the [CC BY 4.0 license](https://creativecommons.org/licenses/CC BY 4.0).

Original provider: PRBO Conservation Science

Dataset credits: The projects were conducted under the grants awarded to the following organizations and their scientists.

The principle investigators of the CalCOFI part of this dataset are (in the chronological order from 1987 to 2006): Richard Veit and John McGowan, Scripps Institution of Oceanography (1987-1994) David Hyrenbach, Scripps Institution of Oceanography (1994-2000) Bill Sydeman, PRBO Conservation Science (2000-2006)

The principle investigators of the Rockfish part of this dataset is Bill Sydeman, PRBO Conservation Science (1996-2006)

the affiliations are the ones they belonged to at the time of the surveys.

The data were contributed by PRBO Conservation Science. These two projects are on going. See [Supplemental information] for the information on the PIs and organizations in recent years.

Abstract: This dataset contains observation data of marine birds and mammals from California Cooperative Oceanic Fisheries Investigations (CalCOFI) from 1987-2006 and Rockfish cruises along the California coast from 1996-2006 by National Marine Fisheries Service (NMFS).

Data were collected aboard research vessels using standardized marine bird and mammal survey techniques (Tasker et al. 1984, Buckland et al. 1993). Marine birds and mammals were observed in a 90-degree arc from the bow to one side of the ship out to 300m. Counts are summarized by species and behavior along the transects in 3 km bins. Data span years 1987 - 2006.

Bottle data collected during CalCOFI cruises 1601, 1604, 1607, and 16011, January 2016 - November 2016. The California Cooperative Oceanic Fisheries Investigations (CalCOFI) are a unique partnership of the California Department of Fish & Wildlife, NOAA Fisheries Service, and Scripps Institution of Oceanograhpy. The organization was formed in 1949 to study the ecological aspects of the sardine population collapse off California. Today our focus has shifted to the study of the marine environment off the coast of California, the management of its living resources, and monitoring the indicators of El Nino and climate change. CalCOFI conducts quarterly cruises off southern & central California, collecting a suite of hydrographic and biological data on station and underway.

The fish larvae (ichthyoplankton) survey is conducted through the California Cooperative Fisheries Investigations program (CALCOFI, http://www.calcofi.org/). These data are a time series of fish larvae counts (or density, as number per 10 m2 of ocean surface) collected in the area of the California Current between San Diego and Avila Beach, California, during the period of 1966 to 2015. Original data were filtered to facilitate consistent comparisons over time and space.

The original CalCOFI fish larvae count data is available from the CoastWatch West Coast Regional Node (WCRN) at NOAA’s Pacific Fisheries Environmental Laboratory, http://coastwatch.pfeg.noaa.gov/erddap/tabledap/index.html. The dataset presented here is an aggregation of 31 data files, originally divided alphabetically by taxon (named “CalCOFI Larvae Counts, Scientific Names * to *”). The data were filtered to include only the 66 core stations with a maximum of 1 cruise per season. These 66 core stations have been most frequently sampled in the past and sampling is ongoing.

CalCOFI sampling began in 1949. However, the dataset presented here begins in 1966 to include only samples that were analyzed with techniques that apply the most current and accurate identification of larvae to the species level. As the backlog of samples (i.e., before 1966) is re-examined, this dataset will be augmented with that additional, earlier data.

Fish egg counts and standardized counts for eggs captured in CalCOFI icthyoplankton nets (primarily vertical [Calvet or Pairovet], oblique [bongo or ring nets], and surface tows [Manta nets]). Surface tows are normally standardized to count per 1,000 m3 strained. Oblique tows are normally standardized to count per 10 m2 of surface sampled. This table includes all tows by species, even if zero eggs were captured for the species, i.e., negative tows. The "Egg Counts Positive Tows" table includes only tows where one or more eggs were captured for the species selected by the user.

Main Titile

Bird and mammal observations aboard CalCOFI (1987-2021, ongoing), NMFS (1996-2021, ongoing) and CPR (2003-2006, completed) cruises.

https://images.unsplash.com/photo-1586115457457-b3753fe50cf1?ixlib=rb-1.2.1&q=80&fm=jpg&crop=entropy&cs=tinysrgb&dl=gerald-schombs-8DO2XXCoB0Q-unsplash.jpg">

Data

The data included in this dataset are bird and mammal observations from aboard research cruises. There are six tables of data: a transect log and observation log pairing for each of the three types of cruises. California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises are conducted quarterly off the coast of southern and central California. National Marine Fisheries (NMFS) cruises are a part of the Rockfish Recruitment Survey off the coast of southern and central California. Data were also collected aboard North Pacific Continuous Plankton Recorder (NPCPR) cruises from June 2002 through May 2006. Observations of birds and mammals include both number and behavior in addition to temporal and spatial information recorded along the cruise transect. Data are collected in order to research the interdependent aspects of the marine environment, including the effects of natural and human based climate change, and the broad implications and influences of ocean currents, weather patterns, fishing practices and coastal development on marine food webs and ecosystem processes.

Acknowledgements

Farallon Institute Advanced Ecosystem Research CalCOFI - Scripps Institution of Oceanography California Current Ecosystem LTER

Sydeman, Bill ( wsydeman@faralloninstitute.org) CCE LTER Information Manager (ccelter.im@gmail.com)

Additional information on NMFS_cruise_observations.csv

***Species** Column*

Codeset: Farallon Species Description: Farallon Institute species code set.

Code     : Definition

BRPE    : Brown Pelican; bird BRCO    : Brandt; bird PALO     : Pacific Loon; bird BFAL     : Black-footed Albatross; bird NOFU     : Northern Fulmar; bird STSH     : Short-tailed Shearwater; bird BVSH     : Black-vented Shearwater; bird LHSP     : Leach; bird FTSP     : Fork-tailed Storm-Petrel; bird PECO     : Pelagic Cormorant; bird RTLO     : Red-throated Loon; bird REPH     : Red Phalarope; bird RNPL     : Red-necked Phalarope; bird EAGR     : Eared Grebe; bird WEGR     : Western Grebe; bird CLGR     : Clarks Grebe; bird POJA      : Pomarine Jaeger; bird LTJA     : Long-tailed Jaeger; bird HEEG     : Heermann's Gull; bird HEGU     : Herring Gull; bird GWGU     : Glaucus-winged Gull; bird WEGU     : Western Gull; bird CAGU     : California Gull; bird BOGU     : Bonaparte; bird ROTE      : Royal Tern; bird BLKI      : Black-legged Kittiwake; bird COMU     : Common Murre; bird RHAU     : Rhinoceros Auklet; bird CAAU     : Cassins Auklet; bird HYGU     : Hybrid Gull; bird WE/CLGR    : Western or Clarks Grebe; bird GW/WEGU   : Glaucus-winged or Western Gull; bird UnID Alcids   : Unidentified Alcids; bird Tern Spp    : Tern species; bird Jaegar Spp    : Jaegar species; bird Phal Spp    : Phalarope species; bird UNCE      : unknown dolphin; mammal CBWH      : Cuviers beaked whale; mammal BBWH      : Bairds beaked whale or Blainville's beaked whale; mammal BLWH      : Blue whale; mammal FIWH       : Fin whale; mammal SEWH      : Sei whale; mammal HUWH      : Humpback whale; mammal SPWH      : Sperm whale; mammal MIWH      : Minke whale; mammal GRWH      : Gray whale; mammal PSWH      : Pygmy sperm whale; mammal DSWH      : dwarf sperm whale; mammal UNWH      : Unknown whale; mammal KIWH      : Killer whale; mammal PIWH/SFP    : Short finned pilot whale; mammal FKWH      : False killer whale; mammal CODO      : Common dolphin; mammal LBCD      : Long-beaked common dolphin; mammal SBCD      : Short-beaked common dolphin; mammal PWSD      : Pacific white-sided dolphin; mammal RIDO       : Risso NRWD      : Northern right whale dolphin; mammal BODO      : Bottlenose dolphin; mammal STDO      : Striped dolphin; mammal UNDO      : Unknown dophin; mammal CAPO      : Dalls porpoise; mammal HAPO      : Harbor porpoise; mammal HASE      : Harbor seal; mammal CASL      : California sea lion; mammal GFSE      : Guadalupe fur seal; mammal NESE      : Northern elephant seal; mammal NFSE      : Northern fur seal; mammal; mammal UNPI      : Unknown pinniped; mammal ANMU     : Ancient Murrelet; bird ARTE      : Arctic Tern; bird ASSP      : Ashy Storm-Petrel; bird
***Behavior** Columns*

Codeset: Farallon Animal Behavior Description: Farallon Institute bird and mammal survey animal behavior code

Code : Definition

1  : In flight 2  : On/in the water 3  : Feeding; also "on/in the water" but hard to see 4  : Ship following 5  : Ship attracted 6  : Bow-riding

LTER Data System Record

http://dx.doi.or...

Jellyfish data from the California Cooperative Oceanic Fisheries Investigations (CALCOFI) were downloaded from http://data.calcofi.net/zooplankton.html. Data were formatted for the 'Jellyfish Database Initiative' (JEDI), a database of jellyfish data developed by the NCEAS Global Jellies Working Group. Data extend from 1951-1999 and cover the central and southern Califiornian shelf waters.

The (CalCOFI) are a unique partnership of the California Department of Fish and Game, NOAA Fisheries Service and Scripps Institution of Oceanography. The organization was formed in 1949 to study the ecological aspects of the sardine population collapse off California. Today our focus has shifted to the study of the marine environment off the coast of California, the management of its living resources, and monitoring the indicators of El Nino and climate change. CalCOFI conducts quarterly cruises off southern & central California, collecting a suite of hydrographic and biological data on station and underway.

Original provider: Annie Douglas, Cascadia Research Collective

Dataset credits: Annie Douglas, Cascadia Research

Abstract: From July 2004 to April 2008 dedicated visual observers following consistent line-transect methods (Buckland et al., 1993; Kinzey et al., 2003) observed from the CalCOFI platforms on quarterly cruises. Observers used handheld 7X50 reticle Fujinon binoculars to sight, identify, and make school size estimates of cetaceans and pinnipeds encountered along the transect lines between CalCOFI water sampling stations. The southern water sampling stations are set along six, parallel lines running southwest to northeast, with lines increasing in length from north to south (470 – 700 km) and stations occurring every 37 km in coastal and continental shelf waters and every 74 km offshore. Three research vessels were used for the sixteen surveys, Scripps Institution of Oceanography Roger Revelle (2 surveys) and New Horizon (8 surveys) and, NOAA David Starr Jordan (6 surveys), vessel height varied from 8.1-13.2m and survey speed varied from 10 to 12 knots.

Bottle data collected during CalCOFI cruises 1203, 1207, 1210, and 1301, March 2012 - January 2013. The California Cooperative Oceanic Fisheries Investigations (CalCOFI) are a unique partnership of the California Department of Fish & Wildlife, NOAA Fisheries Service and Scripps Institution of Oceanography. The organization was formed in 1949 to study the ecological aspects of the sardine population collapse off California. Today our focus has shifted to the study of the marine environment off the coast of California, the management of its living resources, and monitoring the indicators of El Nino and climate change. CalCOFI conducts quarterly cruises off southern & central California, collecting a suite of hydrographic and biological data on station and underway.

This dataset includes data from the CalCOFI ichthyoplankton database and data from publicly available ERDDAP servers hosted at Southwest Fisheries Science Center. The data include fish species occurrence and distribution, identification and developmental staging of fish and egg stages as well as information about cruises, instruments and platforms used in the CalCOFI program from 1951-10-01 to 2017-04-22. The ERDDAP data is available in CSV format. The raw files were extracted from the SWFSC CalCOFI database and includes documentation that explains each table and how to reconstruct the database schema.

This site contains hydrographic data from 1949-2002. It also has ongoing oceanographic, weather, abiotic and invertebrate (e.g. zooplankton) data and research projects details. Database can be downloaded and PUBLICATIONS link also has a search option to find results and data. Of the multiple ocean transects surveyed only one pertains to the central coast.