Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | Time-at-depth data (to generate histograms) from tagged jumbo squid from R/V R4107, R/V Pacific Storm, Chartered Vessels, R/V cruises in the Monterey Bay vicinity and Gulf of California from 2004-2009 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_471977) |
| Range: | longitude = -123.48 to -111.22°E, latitude = 27.34 to 37.91°N, depth = 0.0 to 1950.0m |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Data Access Form
| Files
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Zoom: ![[The graph you specified. Please be patient.]](https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_471977.png?longitude,latitude,tag_id&.draw=markers&.marker=5%7C5&.color=0x000000&.colorBar=%7C%7C%7C%7C%7C&.bgColor=0xffccccff)
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Attributes {
s {
squid_id {
String bcodmo_name "unknown";
String description "Unique squid identifier.";
String long_name "Squid Id";
String units "dimensionless";
}
tag_id {
Int32 _FillValue 2147483647;
Int32 actual_range 52869, 83052;
String bcodmo_name "tagid";
String description "Unique tag identifier.";
String long_name "Tag Id";
String units "dimensionless";
}
descrip {
String bcodmo_name "brief_desc";
String description "Description of sampling location and time of year. CCS = California Current System; GOC = Gulf of California.";
String long_name "Descrip";
String units "dimensionless";
}
dorsal_mantle_len {
Float32 _FillValue NaN;
Float32 actual_range 0.67, 0.83;
String bcodmo_name "length";
String description "Dorsal mantle length (DML).";
String long_name "Dorsal Mantle Len";
String units "centimeters (cm)";
}
date_start {
Int32 _FillValue 2147483647;
Int32 actual_range 20041025, 20091204;
String bcodmo_name "date_begin";
String description "Year, month, and day when the tag was deployed on the squid in YYYYmmdd format.";
String long_name "Date Start";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 27.34, 37.91;
String axis "Y";
String bcodmo_name "lat_start";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude at the time of deployment. Positive values = North.";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String source_name "lat_start";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -123.48, -111.22;
String axis "X";
String bcodmo_name "lon_start";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude at the time of deployment. Negative values = West.";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String source_name "lon_start";
String standard_name "longitude";
String units "degrees_east";
}
date_end {
Int32 _FillValue 2147483647;
Int32 actual_range 20041102, 20091124;
String bcodmo_name "date_end";
String description "Year, month, and day when the tag detached from the squid in YYYYmmdd format.";
String long_name "Date End";
String units "unitless";
}
lat_end {
Float32 _FillValue NaN;
Float32 actual_range 26.59, 37.65;
String bcodmo_name "lat_end";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude at the time the tag detached. Positive values = North.";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "decimal degrees";
}
lon_end {
Float32 _FillValue NaN;
Float32 actual_range -123.99, -109.87;
String bcodmo_name "lon_end";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude at the time the tag detached. Negative values = West.";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "decimal degrees";
}
sampling_time {
Float32 _FillValue NaN;
Float32 actual_range 2.7, 17.6;
String bcodmo_name "time_elapsed";
String description "Total number of sampling days.";
String long_name "Sampling Time";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
String units "number of days";
}
max_depth {
Int16 _FillValue 32767;
Int16 actual_range 400, 1400;
String bcodmo_name "depth_max";
String description "Maximum depth achieved by squid.";
String long_name "Max Depth";
String units "meters (m)";
}
recovered {
String bcodmo_name "unknown";
String description "Indicates if the tag was physically recovered.";
String long_name "Recovered";
String units "yes/no";
}
deploy_day {
Byte _FillValue 127;
Byte actual_range 1, 18;
String bcodmo_name "unknown";
String description "Day of total tag deployment starting on Day 1.";
String long_name "Deploy Day";
String units "dimensionless";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 0.0, 1950.0;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Depth.";
String ioos_category "Location";
String long_name "Depth";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
String positive "down";
String standard_name "depth";
String units "m";
}
count_night {
Int16 _FillValue 32767;
Int16 actual_range 0, 531;
String bcodmo_name "unknown";
Float64 colorBarMaximum 100.0;
Float64 colorBarMinimum 0.0;
String description "Number of counts spent in given temperature bin during nighttime (sunset to sunrise). Each count represents 75 seconds.";
String long_name "Count Night";
String units "Number of counts (1 count = 75 seconds)";
}
count_day {
Int16 _FillValue 32767;
Int16 actual_range 0, 451;
String bcodmo_name "unknown";
Float64 colorBarMaximum 100.0;
Float64 colorBarMinimum 0.0;
String description "Number of counts spent in given temperature bin during daytime (sunrise to sunset). Each count represents 75 seconds.";
String long_name "Count Day";
String units "Number of counts (1 count = 75 seconds)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"All data were collected with Mk10-PAT tags (Wildlife Computers, Redmond, WA)
attached to living Humboldt squid (Dosidicus gigas) as described elsewhere
(Gilly et al. 2006). Tags were programmed to sample at 0.5 Hz or 1 Hz. Tags
deployed in Monterey Bay (CCS-1through CCS-6; deployed during OCE-0850839)
were programmed to transmit time series data (75 s intervals = 0.01333 Hz) for
depth, temperature and light to the Argos satellite system. Tags deployed in
the Gulf of California (GOC-1 through GOC-6; deployed during OCE-0526640) were
physically recovered, and the data were subsampled to match the 75 s interval
of the CCS tags. This procedure was also carried out for tag CCS-6 that was
recovered but never reported to Argos.
Mk10 PAT tags measure depth from 0 to 2000 m with a resolution of 0.5 m and
temperature from 0 to +40 degrees C with a resolution of 0.05 degree C. The
tags were used as supplied by the manufacturer without additional calibration.
References:
Gilly, W.F., Zeidberg, L.D., Booth, J.A.T, Stewart, J.S., Marshall, G.,
Abernathy, K., and Bell, L.E. 2012. Locomotion and behavior of Humboldt squid,
Dosidicus gigas, in relation to natural hypoxia in the Gulf of California,
Mexico. The Journal of Experimental Biology, 215, 3175-3190. doi:
[10.1242/jeb.072538](\\\\\"https://dx.doi.org/10.1242/jeb.072538\\\\\").
Gilly, W.F., Markaida, U., Baxter, C.H., Block, B.A., Boustany, A.,
Zeidberg, L., Reisenbichler, K., Robinson, B., Bazzino, G., and Salinas, C.
2006. Vertical and horizontal migrations by the jumbo squid Dosidicus gigas
revealed by electronic tagging. Marine Ecology Press Series, 324, 1-17. doi:
[10.3354/meps324001](\\\\\"https://dx.doi.org/10.3354/meps324001\\\\\").
Stewart, J.S., Field, J.C., Markaida, U., and Gilly, W.F. 2013. Behavioral
ecology of jumbo squid (Dosidicus gigas) in relation to oxygen minimum zones.
Deep Sea Research Part II: Topical Studies in Oceanography, 95, 197-208. doi:
[10.1016/j.dsr2.2012.06.005](\\\\\"https://dx.doi.org/10.1016/j.dsr2.2012.06.005\\\\\").";
String awards_0_award_nid "55203";
String awards_0_award_number "OCE-0850839";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0850839";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "David L. Garrison";
String awards_0_program_manager_nid "50534";
String awards_1_award_nid "55226";
String awards_1_award_number "R/OPCFISH-06";
String awards_1_funder_name "California Sea Grant";
String awards_1_funding_acronym "CASG";
String awards_1_funding_source_nid "402";
String awards_2_award_nid "471705";
String awards_2_award_number "OCE-0526640";
String awards_2_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0526640";
String awards_2_funder_name "NSF Division of Ocean Sciences";
String awards_2_funding_acronym "NSF OCE";
String awards_2_funding_source_nid "355";
String awards_2_program_manager "David L. Garrison";
String awards_2_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Jumbo squid (Dosidicus gigas) time-at-depth data from MK10 PAT tags
California Current System (CCS) & Gulf of California (GOC)
PI: William Gilly (Stanford University)
Version: 22 Nov 2013
NOTE: 1 count represents a 75-second interval
(in count_night and count_day columns)";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2013-11-22T19:07:32Z";
String date_modified "2019-11-14T20:27:18Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.471977.1";
Float64 Easternmost_Easting -111.22;
Float64 geospatial_lat_max 37.91;
Float64 geospatial_lat_min 27.34;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -111.22;
Float64 geospatial_lon_min -123.48;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 1950.0;
Float64 geospatial_vertical_min 0.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-04-20T01:56:01Z (local files)
2024-04-20T01:56:01Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_471977.das";
String infoUrl "https://www.bco-dmo.org/dataset/471977";
String institution "BCO-DMO";
String instruments_0_acronym "MK10 PAT";
String instruments_0_dataset_instrument_description "Mk10-PAT tags (Wildlife Computers, Redmond, WA) were programmed to sample at 0.5 Hz or 1 Hz. Tags deployed in Monterey Bay (CCS-1through CCS-6) were programmed to transmit time series data (75 s intervals = 0.01333 Hz) to the Argos satellite system. Tags deployed in the Gulf of California (GOC-1 through GOC-6) were physically recovered. Mk10 PAT tags measure depth from 0 to 2000 m with a resolution of 0.5 m and temperature from 0 to +40 degrees C with a resolution of 0.05 degree C. The tags were used as supplied by the manufacturer without additional calibration.";
String instruments_0_dataset_instrument_nid "471984";
String instruments_0_description "The Pop-up Archival Transmitting (Mk10-PAT) tag, manufactured by Wildlife Computers, is a combination of archival and Argos satellite technology. It is designed to track the large-scale movements and behavior of fish and other animals which do not spend enough time at the surface to allow the use of real-time Argos satellite tags. The PAT can be configured to transmit time-at-depth and time-at-temperature histograms, depth-temperature profiles, and/or light-level curves. The histogram duration (1 to 24 hours) and bin ranges can also be configured. PAT archives depth, temperature, and light-level data while being towed by the animal. At a user-specified date and time, the PAT actively corrodes the pin to which the tether is attached, thus releasing the PAT from the animal. The PAT then floats to the surface and transmits summarized information via the Argos system. Argos also uses the transmitted messages to provide the position of the tag at the time of release.";
String instruments_0_instrument_name "Wildlife Computers Mk10 Pop-up Archival Tag (PAT)";
String instruments_0_instrument_nid "471924";
String instruments_0_supplied_name "MK10 PAT";
String keywords "bco, bco-dmo, biological, chemical, count, count_day, count_night, data, dataset, date, date_end, date_start, day, deploy, deploy_day, depth, depth_m, descrip, dmo, dorsal, dorsal_mantle_len, end, erddap, lat_end, latitude, len, lon_end, longitude, management, mantle, max, max_depth, night, oceanography, office, preliminary, recovered, sampling, sampling_time, squid, squid_id, start, tag, tag_id, time";
String license "https://www.bco-dmo.org/dataset/471977/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/471977";
Float64 Northernmost_Northing 37.91;
String param_mapping "{'471977': {'lon_start': 'flag - longitude', 'depth_m': 'flag - depth', 'lat_start': 'flag - latitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/471977/parameters";
String people_0_affiliation "Stanford University";
String people_0_person_name "William Gilly";
String people_0_person_nid "51715";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI BCO-DMO";
String people_1_person_name "Shannon Rauch";
String people_1_person_nid "51498";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "Jumbo Squid Physiology,Jumbo Squid Vertical Migration";
String projects_0_acronym "Jumbo Squid Physiology";
String projects_0_description
"This project concerns the ecological physiology of Dosidicus gigas, a large squid endemic to the eastern Pacific where it inhabits both open ocean and continental shelf environments. Questions to be addressed include:
1) How does utilization of the OML by D. gigas vary on both a daily and seasonal basis, and how do the vertical distributions of the OML and its associated fauna vary?
2) What behaviors of squid are impaired by conditions found in the OML, and how are impairments compensated to minimize costs of utilizing this environment? and
3) What are the physiological and biochemical processes by which squid maintain swimming activity at such remarkable levels under low oxygen conditions?
The investigators will use an integrated approach involving oceanographic, acoustic, electronic tagging, physiological and biochemical methods. D. gigas provides a trophic connection between small, midwater organisms and top vertebrate predators, and daily vertical migrations between near-surface waters and a deep, low-oxygen environment (OML) characterize normal behavior of adult squid. Electronic tagging has shown that this squid can remain active for extended periods in the cold, hypoxic conditions of the upper OML. Laboratory studies have demonstrated suppression of aerobic metabolism during a cold, hypoxic challenge, but anaerobic metabolism does not appear to account for the level of activity maintained. Utilization of the OML in the wild may permit daytime foraging on midwater organisms. Foraging also occurs near the surface at night, and Dosidicus may thus be able to feed continuously. D. gigas is present in different regions of the Guaymas Basin on a predicable year-round basis, allowing changes in squid distribution to be related to changing oceanographic features on a variety time scales.
This research is of broad interest because Dosidicus gigas has substantially extended its range over the last decade, and foraging on commercially important finfish in invaded areas off California and Chile has been reported. In addition, the OML has expanded during the last several decades, mostly vertically by shoaling, including in the Gulf of Alaska, the Southern California Bight and several productive regions of tropical oceans, and a variety of ecological impacts will almost certainly accompany changes in the OML. Moreover, D. gigas currently supports the world's largest squid fishery, and this study will provide acoustic methods for reliable biomass estimates, with implications for fisheries management in Mexico and elsewhere.
This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5). This is a Collaborative Research project encompassing three NSF-OCE awards.
Background Publications:
Stewart, J.S., Field, J.C., Markaida, U., and Gilly, W.F. 2013. Behavioral ecology of jumbo squid (Dosidicus gigas) in relation to oxygen minimum zones. Deep Sea Research Part II: Topical Studies in Oceanography, 95, 197-208. doi:10.1016/j.dsr2.2012.06.005.
Gilly, W.F., Zeidberg, L.D., Booth, J.A.T, Stewart, J.S., Marshall, G., Abernathy, K., and Bell, L.E. 2012. Locomotion and behavior of Humboldt squid, Dosidicus gigas, in relation to natural hypoxia in the Gulf of California, Mexico. The Journal of Experimental Biology, 215, 3175-3190. doi: 10.1242/jeb.072538.
Related Project: Physiological limits to vertical migrations of the pelagic, jumbo squid, Dosidicus gigas in the Gulf of California";
String projects_0_end_date "2013-07";
String projects_0_geolocation "Guaymas Basin, Gulf of California, Mexico (27 N 112 W) and Monterey Bay, CA (36 N 123 W)";
String projects_0_name "Hypoxia and the ecology, behavior and physiology of jumbo squid, Dosidicus gigas";
String projects_0_project_nid "2279";
String projects_0_start_date "2009-08";
String projects_1_acronym "Jumbo Squid Vertical Migration";
String projects_1_description
"Description from NSF award abstract:
Inshore and open-ocean (pelagic) squid are the most athletic of all invertebrates. They are highly active, jet-propelled swimmers, have high metabolic rates and grow at a prodigious rate throughout their short life spans of one to two years. Such squid are abundant in all the world's oceans where they play important ecological roles as major predators. Adult squid serve as essential prey for many top predators, including sharks, tuna, billfish and marine mammals. In addition, squid are becoming increasingly important in commercial fisheries worldwide as they replace slow-growing fish, particularly where these stocks are being depleted. Dosidicus gigas, also known as the jumbo or Humboldt squid, is a true giant, reaching 2-3 m in overall length and over 50 kg in mass. It is widely distributed over the eastern Pacific, ranging from Chile to Canada and nearly to Hawaii at the equator. It forms the basis of a major commercial fishery, presently the third largest in Mexico. Despite the ecological and economic importance of D. gigas, little is known about its life history, behavior or physiology. Its large size and open-ocean habitat complicate traditional field and laboratory studies. This project focuses on integrative field and laboratory studies of D. gigas in the Gulf of California using recently developed techniques that facilitate such studies. Pilot tagging studies have revealed that D. gigas spends the daytime in cold, deep, oxygen-depleted water (~10 deg C at 300 meters) and migrates at night to shallow, aerated surface waters that can reach 30 deg C. Frequent rapid dives at night to daytime depths cover several hundred meters in minutes. It is a mystery how these large, metabolically active squid can tolerate the stress of chronic daytime hypoxia at depth. Conversely, warm surface waters also may present a stress that limits the time squid can spend in this zone. This proposal will employ electronic tagging to track vertical migrations of this pelagic predator and to monitor natural jetting and respiration at different depths. Oxygen consumption determined from these data, with calibrations provided by laboratory swim-tunnel experiments and biochemical indices of anaerobic metabolism, will provide a measure of the true energetic costs to the squid itself. Extreme low-light video methods will reveal natural behaviors over the range of a typical vertical migration, both day and night. Thus, this project will reveal what this remarkable squid is doing in its oceanic habitat, why it is doing it, and what physiological and biochemical adaptations permit these behaviors at some depths and preclude them at others.
This study will greatly advance our understanding of the biology of D. gigas and provide a model for an integrated approach to studying the ecological physiology of other pelagic predators. It will also establish a life-history framework that will ultimately be necessary to manage this fishery at the ecosystem level in Mexico and elsewhere.
Related Project: Hypoxia and the ecology, behavior and physiology of jumbo squid, Dosidicus gigas";
String projects_1_end_date "2009-09";
String projects_1_geolocation "Gulf of California";
String projects_1_name "Physiological limits to vertical migrations of the pelagic, jumbo squid, Dosidicus gigas in the Gulf of California";
String projects_1_project_nid "471887";
String projects_1_start_date "2005-09";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 27.34;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Time-at-depth data (to generate histograms) from tagged jumbo squid from R/V R4107, R/V Pacific Storm, Chartered Vessels, R/V cruises in the Monterey Bay vicinity and Gulf of California from 2004-2009";
String title "Time-at-depth data (to generate histograms) from tagged jumbo squid from R/V R4107, R/V Pacific Storm, Chartered Vessels, R/V cruises in the Monterey Bay vicinity and Gulf of California from 2004-2009";
String version "1";
Float64 Westernmost_Easting -123.48;
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.