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Dataset Title:  Descriptive data from Isaacs-Kidd midwater trawls (IKMT) from R/V New Horizon
cruise NH1106 in the Guaymas Basin in 2011 (Jumbo Squid Physiology project)
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_4010)
Range: longitude = -113.0509 to -111.3798°E, latitude = 27.2981 to 28.6382°N, depth = 246.0 to 960.0m
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Subset | Data Access Form | Files
 
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Things You Can Do With Your Graphs

Well, you can do anything you want with your graphs, of course. But some things you might not have considered are:

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  cruise_id {
    String bcodmo_name "cruise_id";
    String description "Cruise identifier.";
    String long_name "Cruise Id";
    String units "text";
  }
  instrument {
    String bcodmo_name "instrument";
    String description "Type of sampling instrument. IKMT = Isaacs-Kidd midwater trawl.";
    String long_name "Instrument";
    String units "text";
  }
  tow {
    Byte _FillValue 127;
    Byte actual_range 1, 21;
    String bcodmo_name "tow";
    String description "Tow number.";
    String long_name "Tow";
    String units "integer";
  }
  location {
    String bcodmo_name "site_descrip";
    String description "General location of sampling.";
    String long_name "Location";
    String units "text";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float64 _FillValue NaN;
    Float64 actual_range 27.2981, 28.6382;
    String axis "Y";
    String bcodmo_name "lat_start";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "Latitude at start of tow.";
    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 -113.0509, -111.3798;
    String axis "X";
    String bcodmo_name "lon_start";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "Longitude at start of tow.";
    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";
  }
  target_depths {
    String bcodmo_name "depth";
    String description "Target depth(s).";
    String long_name "Target Depths";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
    String units "meters";
  }
  target_depth_min {
    Int16 _FillValue 32767;
    Int16 actual_range 10, 380;
    String bcodmo_name "depth_min";
    String description "Minimum of the target depth(s).";
    String long_name "Target Depth Min";
    String units "meters";
  }
  target_depth_max {
    Int16 _FillValue 32767;
    Int16 actual_range 20, 380;
    String bcodmo_name "depth";
    String description "Maximum of the target depth(s).";
    String long_name "Target Depth Max";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
    String units "meters";
  }
  day_or_night {
    String bcodmo_name "time_of_day";
    String description "Time of day (Day or Night).";
    String long_name "Day Or Night";
    String units "text";
  }
  depth_btm_min {
    String bcodmo_name "depth_bottom";
    String description "Minimum bottom depth. (Note: gt = \"greater than\")";
    String long_name "Depth";
    String standard_name "depth";
    String units "meters";
  }
  depth {
    String _CoordinateAxisType "Height";
    String _CoordinateZisPositive "down";
    Float64 _FillValue NaN;
    Float64 actual_range 246.0, 960.0;
    String axis "Z";
    String bcodmo_name "depth_bottom";
    String description "Maximum bottom depth. (Note: gt = \"greater than\")";
    String ioos_category "Location";
    String long_name "Depth";
    String positive "down";
    String standard_name "depth";
    String units "m";
  }
  date_start {
    String bcodmo_name "date_begin";
    String description "Date when the net entered the water (GMT) in mm/dd/YYYY format.";
    String long_name "Date Start";
    String source_name "date_start";
    String time_precision "1970-01-01";
    String units "unitless";
  }
  time_start {
    String bcodmo_name "time_start";
    String description "Time when the net entered the water (UTC).";
    String long_name "Time Start";
    String units "HH:MM";
  }
  time_end {
    String bcodmo_name "time_end";
    String description "Time when the net exited the water (UTC).";
    String long_name "Time End";
    String units "HH:MM";
  }
  time_start_target_depth {
    String bcodmo_name "time_begin";
    String description "Start time at target depth (UTC).";
    String long_name "Time Start Target Depth";
    String units "HH:MM";
  }
  time_end_target_depth {
    String bcodmo_name "time_end";
    String description "Stop time at target depth (UTC).";
    String long_name "Time End Target Depth";
    String units "HH:MM";
  }
  sog_min {
    Float32 _FillValue NaN;
    Float32 actual_range 3.0, 4.3;
    String bcodmo_name "sog";
    String description "Minimum speed over ground.";
    String long_name "Sog Min";
    String units "knots";
  }
  sog_max {
    Float32 _FillValue NaN;
    Float32 actual_range 3.7, 4.8;
    String bcodmo_name "sog";
    String description "Maximum speed over ground.";
    String long_name "Sog Max";
    String units "knots";
  }
  wire_out_max {
    Int16 _FillValue 32767;
    Int16 actual_range 75, 1250;
    String bcodmo_name "wire_out";
    String description "Maximum wire out.";
    String long_name "Wire Out Max";
    String units "meters";
  }
  portion_cod_end_filled {
    String bcodmo_name "unknown";
    String description "Portion (fraction) of cod end filled. (Note: lt = \"less than\")";
    String long_name "Portion Cod End Filled";
    String units "fraction";
  }
  pcnt_catch_preserved {
    Float32 _FillValue NaN;
    Float32 actual_range 50.0, 100.0;
    String bcodmo_name "unknown";
    String description "Percent of catch preserved.";
    String long_name "Pcnt Catch Preserved";
    String units "percent (%)";
  }
  no_jars_preserved {
    Byte _FillValue 127;
    Byte actual_range 1, 2;
    String bcodmo_name "unknown";
    String description "Number of jars preserved.";
    String long_name "No Jars Preserved";
    String units "integer";
  }
  notes {
    String bcodmo_name "comment";
    String description "Free-text notes about the tow.";
    String long_name "Notes";
    String units "text";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
    String acquisition_description 
"Tows with a 2m x 2m Isaacs-Kidd Midwater trawl (IKMT), 7m in length, with a
1mm mesh were conducted periodically throughout the cruise. The net was fitted
with a Simrad PI depth sensor that provides net depth information in real time
acoustically. Trawls were targeted to depths of interest based on acoustic
sampling with the goal of achieving 20 minutes of towing time at the target
depth at a target speed of 4 knots. Samples were preserved in 5% buffered
formalin in seawater and are archived in the biocuration facility at Oregon
State University.";
    String awards_0_award_nid "55202";
    String awards_0_award_number "OCE-0851239";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0851239";
    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 cdm_data_type "Other";
    String comment 
"NH1106 Midwater Trawl 
  Guaymas Basin, Gulf of California 
 PI: Kelly Benoit-Bird (OSU) 
 Version: 08 Aug 2013";
    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 "2013-08-08T18:56:17Z";
    String date_modified "2019-11-12T20:58:32Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.4010.1";
    Float64 Easternmost_Easting -111.3798;
    Float64 geospatial_lat_max 28.6382;
    Float64 geospatial_lat_min 27.2981;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -111.3798;
    Float64 geospatial_lon_min -113.0509;
    String geospatial_lon_units "degrees_east";
    Float64 geospatial_vertical_max 960.0;
    Float64 geospatial_vertical_min 246.0;
    String geospatial_vertical_positive "down";
    String geospatial_vertical_units "m";
    String history 
"2021-10-15T19:52:04Z (local files)
2021-10-15T19:52:04Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_4010.das";
    String infoUrl "https://www.bco-dmo.org/dataset/4010";
    String institution "BCO-DMO";
    String instruments_0_acronym "IKMT";
    String instruments_0_dataset_instrument_description "IKMT with 2-meter by 2-meter mouth opening; 7 meters in length.";
    String instruments_0_dataset_instrument_nid "6239";
    String instruments_0_description 
"A trawl with a pentagonal mouth opening and a dihedral depressor vane as part of the mouth opening. IKMTs come in various dimensions (refer to individual dataset documentation).

The original IKMTs were 10 foot (304 cm) and 15 foot (457 cm) at the mouth. The 10 foot IKMT net was 31 feet (9.45 m) in length (Wiebe and Benfield 2003).";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/NETT0071/";
    String instruments_0_instrument_name "Isaacs-Kidd Midwater Trawl";
    String instruments_0_instrument_nid "715";
    String instruments_0_supplied_name "Isaacs-Kidd Midwater Trawl";
    String keywords "bco, bco-dmo, biological, catch, chemical, cod, cruise, cruise_id, data, dataset, date, day, day_or_night, depth, depth_btm_max, depth_btm_min, depths, dmo, end, erddap, filled, instrument, jars, latitude, longitude, management, max, min, night, no_jars_preserved, notes, oceanography, office, out, pcnt, pcnt_catch_preserved, portion, portion_cod_end_filled, preliminary, preserved, sog, sog_max, sog_min, start, target, target_depth_max, target_depth_min, target_depths, time, time_end, time_end_target_depth, time_start, time_start_target_depth, tow, wire, wire_out_max";
    String license "https://www.bco-dmo.org/dataset/4010/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/4010";
    Float64 Northernmost_Northing 28.6382;
    String param_mapping "{'4010': {'lat_start': 'flag - latitude', 'lon_start': 'flag - longitude', 'depth_btm_max': 'flag - depth'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/4010/parameters";
    String people_0_affiliation "Oregon State University";
    String people_0_affiliation_acronym "OSU-CEOAS";
    String people_0_person_name "Kelly Benoit-Bird";
    String people_0_person_nid "51716";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Oregon State University";
    String people_1_affiliation_acronym "OSU-CEOAS";
    String people_1_person_name "Chad Waluk";
    String people_1_person_nid "51717";
    String people_1_role "Contact";
    String people_1_role_type "related";
    String people_2_affiliation "Woods Hole Oceanographic Institution";
    String people_2_affiliation_acronym "WHOI BCO-DMO";
    String people_2_person_name "Shannon Rauch";
    String people_2_person_nid "51498";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "Jumbo Squid Physiology";
    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 publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 27.2981;
    String standard_name_vocabulary "CF Standard Name Table v55";
    String subsetVariables "cruise_id,instrument";
    String summary "Sampling locations, depths, times, etc. from midwater trawls performed on the NH1106 cruise in the Guaymas Basin. Samples are archived in the biocuration facility at Oregon State University.";
    String title "Descriptive data from Isaacs-Kidd midwater trawls (IKMT) from R/V New Horizon cruise NH1106 in the Guaymas Basin in 2011 (Jumbo Squid Physiology project)";
    String version "1";
    Float64 Westernmost_Easting -113.0509;
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

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.


 
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