Data Set Citation

When using this data, please cite the data package
California Cooperative Oceanic Fisheries Investigations.
Jellyfish Data - California Cooperative Oceanic Fisheries Investigations
klr.28.5 (https://knb.ecoinformatics.org/knb/metacat/klr.28.5/knb)

General Information
Title:Jellyfish Data - California Cooperative Oceanic Fisheries Investigations
Identifier:klr.28
Abstract:
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.
Keywords:
  • Jellyfish
  • CALCOFI
  • California Current
  • Cnidaria
  • Salp
  • Ctenophora
  • temperate

Data Table, Image, and Other Data Details:
Metadata download Ecological Metadata Language (EML) File
Data Table:JEDI Template.txt ( View Metadata )

Involved Parties

Data Set Creators
Organization:California Cooperative Oceanic Fisheries Investigations
Address:
California USA
Web Address:
http://data.calcofi.net/zooplankton.html

Data Set Contacts
Individual:Dr. Marc Ohman
Organization:Scripps Institute of Oceanography
Address:
9500 Gilman Dr, Dept 0218,
La Jolla, California 92093-0218 USA
Phone:
858-534-2754 (voice)
Email Address:
mohman@ucsd.edu

Associated Parties
Individual: Kelly Robinson
Organization:Dauphin Island Sea Lab
Position:PhD Candidate
Address:
101 Bienville Blvd.,
Dauphin Island, AL 36528 USA
Phone:
(251) 861-2289 (voice)
Email Address:
krobinson@disl.org
Individual:Dr. William 'Monty' Graham
Organization:Dauphin Island Sea Lab
Position:Senior Marine Scientist II
Address:
101 Bienville Blvd.,
Dauphin Island, AL 36528 USA
Phone:
(251) 861-2141 ext. 2272 (voice)
Email Address:
mgraham@disl.org
Individual:Dr. Carlos Duarte
Organization:Instituto Mediterráneo de Estudios Avanzados
Position:Profesor de investigación
Address:
C/ Miquel Marquès, 21,
07190 Esporles,
Islas Baleares, Spain
Phone:
+34 971611725 (voice)
Email Address:
carlosduarte@imedea.uib-csic
Individual:Dr. Robert Condon
Organization:Dauphin Island Sea Lab
Position:Faculty Research Scientist
Address:
101 Bienville Blvd.,
Dauphin Island, AL 36528 USA
Phone:
(251) 861-2141 x 7546 (voice)
Email Address:
rcondon@disl.org

Data Set Characteristics

Geographic Region:
Geographic Description:Central and southern California shelf waters. See http://calcofi.org/cb-aboutcalcofi/art-overview.html for more complete description and access to reports explaining differences in spatial cover over the time-series.
Bounding Coordinates:
West:  -127.375  degrees
East:  -116.625  degrees
North:  39.75  degrees
South:  30.875  degrees
Time Period:
Begin:
1951
End:
1999
Taxonomic Range:
Classification:
Rank Name:Phylum
Rank Value:Chordata
Classification:
Rank Name:Phylum
Rank Value:Cnidaria
Classification:
Rank Name:Phylum
Rank Value:Ctenophora

Sampling, Processing and Quality Control Methods

Step by Step Procedures
Step 1:  
Description:

Sample collection

The maximum zooplankton sampling depth in the CalCOFI time series increased from 0-70 m (1949-1950) to 0-140 m in 1951. It was maintained at 0-140 m from 1951-1968, and then increased to 0-210 m in 1969, where it has since remained (see Ohman and Smith 1995). A 1-m diameter ring net was used from 1949 - late 1977, which was then replaced with a 0.71-m diameter bongo net in December 1977 (Ohman and Smith 1995). Effects of these changes have been analyzed by Brinton and Townsend (1981), Ohman and Smith (1995), Rebstock (2001), and Ohman and Lavaniegos (2002). Results suggest that only some species of euphausiids (Brinton and Townsend 1981) and salps (Ohman and Lavaniegos 2002) are caught differentially by the two nets. A net correction factor can be applied if desired. See ZooDB Correction Factors.

* Bongo or CalBOBL Net - two circles, 0.71 m in diameter, with a central yoke which connects to the towing cable. The nets are 3 m in length, a 1.5 m cylindrical portion joined to 1.5 m conical portion tapering to a detachable cod end. At least one (starboard net), the principal ichthyoplankton sample net, is made from 0.505 mm square mesh nylon. The sample from the port side net is used for other purposes; the mesh size is either 0.505 mm or 0.333 mm depending on requirements. The cod end of each net is constructed of 0.333 mm mesh. The ratio of mesh aperture area to mouth area is 4.8:1 for the 0.505 mesh net.

Plankton samples are obtained by retrieving the sampler at an oblique angle. A 22 kg weight is attached to the bottom of yoke frame. While the survey ship is making 1-2 knots, a fixed amount of towing cable is paid out, the net is held at depth for 30 seconds and then retrieved at a constant rate (20 m/min). Ship speed is adjusted to maintain the towing cable at a constant angle to the vertical ( 45 degrees +/- 3 degrees). During each plankton tow 300 m of towing cable is paid out; thus the vertical depth sampled is approximately 210 m. In shallow areas the amount of towing cable paid out is adjusted so that the net fished to approximately 15 m off the bottom.
Instrument(s): * Pairovet or CalVET- 0.25 m in diameter pair; the nets are 1.5 m in length, a 0.8 m cylindrical portion joined to 0.6 m conical portion tapering to a 0.1 m cod end.
Instrument(s): o 1980 - 1982: net was 0.333 mm square mesh nylon;
Instrument(s): o 1983 - 1985: net was 0.150 mm square mesh nylon.
Instrument(s): The ratio of mesh aperture area to mouth area is about 8:1.
Instrument(s): Egg samples are obtained by vertically retrieving the net. A 45 kg weight is attached to the end of the towing cable, a few meters below the sampler. With the survey ship holding a stationary position, 70 m of towing cable was paid out, the net was held at depth for 10 seconds and then retrieved vertically at a rate of 70 m/min. The angle of stray from the vertical was not allowed to exceed 15 degrees
Instrument(s): * MANTA -The twin winged continuous-flow surface tow, is used for samples on the ocean surface minimizing wake disturbance from the ship. The MANTA Net is an improved design from the Neuston Net and is capable of continuous-flow collection of organisms at the ocean surface. The frame is supported at the ocean surface by a pair of aquaplanes projecting at right angles from the paravanes. The net is towed by a wire yoke with one short bridle and one long bridle in order to angle the net from the ship. The net is nylon, nominally .505 mm square mesh with a 333 codend.
Instrument(s): * Other Nets:
Instrument(s): o CAL1MOBL - standard CALCOFI plankton sampler from 1951 through 1978.
Instrument(s): 1-meter in diameter, net (approximately 4 m) was attached.
Instrument(s): o MOCNESS - is used for specialized tows for zooplankton. The MOCNESS or Multiple Opening/Closing Net and Environmental Sensing System is based on the Tucker Trawl principle and is manufactured by Biological Environmental Sampling Systems (B.E.S.S.). M1 is a 1 meter frame with 10 nets. M2 is a 10 meter frame with six nets."
Step 2:  
Description:

Formatting for incorporation into JEDI

http://data.calcofi.net/zooplankton.html

Save data from CalCOFI database

Import into Excel

Change month number to word

Change Day/Night

Day to 12:00:00 (Day was classified as the time between Nautical sunrise and sunset)

Night to 00:00:00 (Day was classified as the time between Nautical sunset and sunrise)

Removed Region, Tow, and Pooled/Unpooled data. Seen as irrelevant.

Added

Net Opening, found in Materials and Methods

Net Mesh, found in net information

Integrated depth, included in dataset obtained from ZooDB as search parameter

Numeric integrated, included in dataset obtained from ZooDB as search parameter

Project Title, CalCOFI Zooplankton Data Base

Project Owner, California Cooperative Oceanic Fisheries Investigations

Contact, Dr. Mark D. Ohman

Taxon, provided in ZooDB as search parameter

Phylum, found on http://www.itis.gov, when applicable

Class, found on http://www.itis.gov, when applicable

Order, found on http://www.itis.gov, when applicable

Family, found on http://www.itis.gov, when applicable

Genus, found on http://www.itis.gov, when applicable

Species, some provided in ZooDB as search parameter

Data Type, Quantitative based on numeric abundance of Zooplankton

Collection Method, plankton net

6 Nov 2010 - Kelly Robinson

Presence_Absence JEDI field

#All records with '0.00' values in the fields 'numeric_density' and 'depth_integrated_density' were denoted as 'absent.'

#All records with values greater than '0.00' in the fields 'numeric_density' and 'depth_integrated_density' were denoted as 'present.'

Formatting for JEDI

#Changed owner from Dr. Marc Ohman to 'California Cooperative Oceanic Fisheries Investigations.'

#Ran the 'jedi-prep' R validation script.

#Kicked back error message about the 'is_public' field failing a 'boolan' test. Couldn't find anything wrong with field or values in column. Not sure what that means so wrote Jim Regetz. Jim's response: First, the data set is failing a 'boolean test,' not a 'boolan' test. Whoops for typo in program. Second, data set failed validation because the only values accepted in the 'is_public' field are (T, TRUE, F, FALSE).

#Records with no values in 'numeric_density" and "depth_integrated_density" in the Excel file "CalCOFI_JEDI_dataset_6Nov2010_KR.xls" deleted. Looked like they left over duplicates from when Stacy combined records with only 'numeric_density' or 'depth_integrated_density' values into a single record that had values for both fields.

#Deleted records saved in a separate Excel file 'Deleted records from CalCOFI_JEDI_dataset_6Nov2010_KR.xls"

#Added 13 records of Salpa maxima from day sampling that were missing.

#Removed genus names from 'species' field.

#Numeric_density values in original data set from the web are given as (no/1000m3). Divided all values by 1000 to yield (no/m3).
Sampling Area And Frequency:
Gelatinous zooplankton collected in from 1951-present in the Central and Southern California Bight.
Sampling Description:
CalCOFI data http://www.calcofi.org/ https://oceaninformatics.ucsd.edu/zoodb/\ "Methods Notes Changes in Sampling Methods and Geographic Coverage The user should be aware that both the geographic coverage and temporal frequency of CalCOFI cruises have changed since the program was initiated in 1949. It is essential that users of ZooDB carefully consider the changing spatial coverage of cruises (see CalCOFI station occupation), as well as the cruises for which particular taxa have been analyzed (Table 1 - Southern California Coverage and Table 2 - Central California Coverage), prior to generating time series of abundance of any organisms. The maximum zooplankton sampling depth in the CalCOFI time series increased from 0-70 m (1949-1950) to 0-140 m in 1951. It was maintained at 0-140 m from 1951-1968, and then increased to 0-210 m in 1969, where it has since remained (see Ohman and Smith 1995). A 1-m diameter ring net was used from 1949 - late 1977, which was then replaced with a 0.71-m diameter bongo net in December 1977 (Ohman and Smith 1995). Effects of these changes have been analyzed by Brinton and Townsend (1981), Ohman and Smith (1995), Rebstock (2001), and Ohman and Lavaniegos (2002). Results suggest that only some species of euphausiids (Brinton and Townsend 1981) and salps (Ohman and Lavaniegos 2002) are caught differentially by the two nets. A net correction factor can be applied if desired. See ZooDB Correction Factors. M.D. Ohman's retrospective studies have focused on interannual variability in springtime cruises, hence more up-to-date temporal coverage is available for springtime cruises than at other times of year. The zooplankton samples for this study were enumerated as either individual samples ("unpooled") or after combining aliquots corresponding to 50 m3 of water filtered from each of several samples taken in a common geographic area ("pooled" samples). Pooled samples were composed only from nighttime stations (i.e., between nautical sunset and nautical sunrise), from two regions defined as Southern California (CalCOFI lines 80 through 93, from shore through station 70) and Central California (CalCOFI lines 60 through 70, from shore through station 90; see coverage map) by Lavaniegos and Ohman (2007). See Rebstock (2001) and Lavaniegos and Ohman (2002) for pooling techniques and Table 1 - Southern California Coverage and Table 2 - Central California Coverage for taxa analyzed for each cruise. Literature citations are available at the References tab.

Data Set Usage Rights

Usage restricted to Global Jellies Working Group members.
Access Control:
Auth System:knb
Order:denyFirst
Additional Metadata
Additional Metadata
Additional Metadata
Additional Metadata
Additional Metadata
Metadata download Ecological Metadata Language (EML) File