Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | [Pump mesozooplankton samples] - Mesozooplankton sample data from R/V Pelican cruises PE03-NGOMEX, PE04-NGOMEX, PE06-NGOMEX, PE07-NGOMEX, PE09-05 in the Northern Gulf of Mexico from 2003-2008 (NGOMEX - Living Marine Resources of the Northern Gulf of Mexico) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_746107) |
| Information: | Summary
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| FGDC
| ISO 19115
| Metadata
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Attributes {
s {
ctd {
String bcodmo_name "cast";
String description "CTD profile ID / start time";
String long_name "CTD";
String units "unitless";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -93.65449, -89.47567;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "longitude immediately preceeding CTD cast";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees_east";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 28.39068, 29.6996;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "latitude immediately preceeding CTD cast";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees_north";
}
time {
String _CoordinateAxisType "Time";
Float64 actual_range 1.059584835e+9, 1.218507544e+9;
String axis "T";
String bcodmo_name "ISO_DateTime_UTC";
String description "Timestamp (UTC) in standard ISO 8601:2004(E) format YYYY-mm-ddTHH:MM:SSZ";
String ioos_category "Time";
String long_name "ISO Date Time UTC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/";
String source_name "ISO_DateTime_UTC";
String standard_name "time";
String time_origin "01-JAN-1970 00:00:00";
String time_precision "1970-01-01T00:00:00Z";
String units "seconds since 1970-01-01T00:00:00Z";
}
d_min {
Float32 _FillValue NaN;
Float32 actual_range 4.5, 5.45;
String bcodmo_name "time_elapsed";
String description "sampling duration, elapsed minutes";
String long_name "D Min";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
String units "minutes";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 1.1, 33.1;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "sampling depth (± ~1.5 m)";
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";
}
bottom {
Float32 _FillValue NaN;
Float32 actual_range 2.58, 50.52;
String bcodmo_name "depth_bottom";
String description "bottom depth (± ~1.5 m)";
String long_name "Bottom";
String units "decibars (dbar)";
}
s_per_50l {
Float32 _FillValue NaN;
Float32 actual_range 9.0, 19.1375;
String bcodmo_name "flow_rate";
String description "inverse of flow rate (time to pump 50 l) (± ~40%)";
String long_name "s per 50l";
String units "seconds (s)";
}
mesh {
Int16 _FillValue 32767;
Int16 actual_range 64, 500;
String bcodmo_name "net_mesh";
String description "sieve mesh size fraction (64 and either 200 or 500 µm)";
String long_name "Mesh";
String units "micrometers (µm)";
}
splits {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 0, 5;
String bcodmo_name "sample_descrip";
String description "number of times sample was halved by plankton splitter";
String long_name "Splits";
String units "unitless";
}
beaker {
Int16 _FillValue 32767;
Int16 actual_range 5, 2000;
String bcodmo_name "sample_descrip";
String description "remaining sample volume after splits";
String long_name "Beaker";
String units "milliliters (ml)";
}
aliquot {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 5, 10;
String bcodmo_name "volume";
String description "volume examined under microscope";
String long_name "Aliquot";
String units "milliliters (ml)";
}
replicate {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 0, 3;
String bcodmo_name "replicate";
String description "name for replicate aliquots";
String long_name "Replicate";
String units "unitless";
}
vol {
Float32 _FillValue NaN;
Float32 actual_range 7.17e-4, 1.25;
String bcodmo_name "volume";
String description "sample volume for in situ concentration estimates. See methodology for the formula used to calculate volume.";
String long_name "Vol";
String units "cubic meters (m^3)";
}
ID {
String bcodmo_name "taxon";
String description "taxonomic group";
String long_name "ID";
String units "unitless";
}
length {
Float32 _FillValue NaN;
Float32 actual_range 0.05, 10.0;
String bcodmo_name "length";
String description "length (to nearest 0.05 mm)";
String long_name "Length";
String units "millimeters (mm)";
}
width {
Float32 _FillValue NaN;
Float32 actual_range 0.05, 4.0;
String bcodmo_name "width";
String description "width (to nearest 0.05 mm)";
String long_name "Width";
String units "millimeters (mm)";
}
adj_count {
Float32 _FillValue NaN;
Float32 actual_range 1.0, 104.0;
String bcodmo_name "unknown";
Float64 colorBarMaximum 100.0;
Float64 colorBarMinimum 0.0;
String description "total count divided among length, width measurements";
String long_name "Adj Count";
String units "unitless";
}
flag {
Int16 _FillValue 32767;
Int16 actual_range 0, 345;
String bcodmo_name "flag";
Float64 colorBarMaximum 150.0;
Float64 colorBarMinimum 0.0;
String description "flag (see methodology for flag codes)";
String long_name "Flag";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
String acquisition_description
"Methodology:
Plankton samples were collected from discrete depths during CTD casts using
a high-capacity, diaphragm pump with an intake hose mounted to the CTD
Rosette. Subsamples of sample contents were manually counted, identified, and
measured in the laboratory
Sampling and analytical procedures:
For each sample, the pump was run for a timed period of nominally 5 min. The
flow rate of the pump was usually measured immediately prior to sampling, by
recording the time required to fill a barrel of known volume. Samples were
preserved and stored in 5% buffered formalin. The laboratory protocol was to
separate samples into two size fractions by passing them through large (200 or
500 \\u03bcm) then small (64 \\u03bcm) mesh sieves; split, dilute, and sub-
sample each size fraction as needed; count and identify all plankters (minimum
n = 50) in each subsample; and estimate the length and width of exactly 100
plankters (the first 50 from the large and small fraction, respectively) to
the nearest 50 \\u03bcm using a dissecting microscope. Three replicate small
size fractions per sample were processed starting in 2006.
Data column \"vol\" was calculated as follows:
vol =
length(unique(replicate)*aliquot/beaker/2^splits*50/s_per_50l*d_min*60*1e-3
Data column \"flag\" contains the following codes:
flag 1: length & width were not measured, but estimated from similar samples
flag 2: shallow & deep samples not labeled, but deduced from sample contents
flag 3: depth estimate less accurate than usual (\\u00b1 ~3 m)
flag 4: time estimate less accurate than usual (\\u00b1 ~15 min)
flag 5: pump flow rate estimated by nominal flow rate";
String awards_0_award_nid "54725";
String awards_0_award_number "OCE-1043261";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1043261";
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 "54830";
String awards_1_award_number "OCE-1043248";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1043248";
String awards_1_funder_name "NSF Division of Ocean Sciences";
String awards_1_funding_acronym "NSF OCE";
String awards_1_funding_source_nid "355";
String awards_1_program_manager "David L. Garrison";
String awards_1_program_manager_nid "50534";
String awards_2_award_nid "54947";
String awards_2_award_number "OCE-1043249";
String awards_2_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1043249";
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 awards_3_award_nid "748455";
String awards_3_award_number "NA06NOS4780148";
String awards_3_data_url "https://grantsonline.rdc.noaa.gov/flows/publicSearch/showAwardDetails.do?awdNum=NA06NOS4780148";
String awards_3_funder_name "National Oceanic and Atmospheric Administration";
String awards_3_funding_acronym "NOAA";
String awards_3_funding_source_nid "352";
String awards_4_award_nid "748458";
String awards_4_award_number "NA09NOS4780198";
String awards_4_data_url "https://grantsonline.rdc.noaa.gov/flows/publicSearch/showAwardDetails.do?awdNum=NA09NOS4780198";
String awards_4_funder_name "National Oceanic and Atmospheric Administration";
String awards_4_funding_acronym "NOAA";
String awards_4_funding_source_nid "352";
String awards_5_award_nid "748463";
String awards_5_award_number "NAS-GRP-2000006418";
String awards_5_data_url "http://www.nas.edu/gulf/grants/grantees/index.htm";
String awards_5_funder_name "Gulf Research Program of the National Academies of Sciences, Engineering, and Medicine";
String awards_5_funding_acronym "GRP";
String awards_5_funding_source_nid "748462";
String cdm_data_type "Other";
String comment
"NGOMEX pump mesozooplankton data
PI: Michael Roman
Data version 1: 2018-10-22";
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 "2018-09-12T17:04:38Z";
String date_modified "2018-11-16T16:00:19Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.749705";
Float64 Easternmost_Easting -89.47567;
Float64 geospatial_lat_max 29.6996;
Float64 geospatial_lat_min 28.39068;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -89.47567;
Float64 geospatial_lon_min -93.65449;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 33.1;
Float64 geospatial_vertical_min 1.1;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-21T12:03:54Z (local files)
2024-11-21T12:03:54Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_746107.html";
String infoUrl "https://www.bco-dmo.org/dataset/746107";
String institution "BCO-DMO";
String instruments_0_acronym "CTD";
String instruments_0_dataset_instrument_nid "747482";
String instruments_0_description "The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column and permits scientists observe the physical properties in real time via a conducting cable connecting the CTD to a deck unit and computer on the ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast. This instrument designation is used when specific make and model are not known.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/130/";
String instruments_0_instrument_name "CTD profiler";
String instruments_0_instrument_nid "417";
String instruments_0_supplied_name "Sea-Bird 9 CTD";
String instruments_1_dataset_instrument_description "220 l/m nominal flow rate, 10 cm intake diameter opening";
String instruments_1_dataset_instrument_nid "747481";
String instruments_1_description "A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps";
String instruments_1_instrument_name "Pump";
String instruments_1_instrument_nid "726";
String instruments_1_supplied_name "Ingersoll-Rand diaphragm pump";
String keywords "50l, adj, adj_count, aliquot, bco, bco-dmo, beaker, biological, bottom, chemical, conductivity, count, ctd, d_min, data, dataset, date, depth, dmo, erddap, flag, iso, latitude, length, longitude, management, mesh, min, oceanography, office, per, preliminary, replicate, s_per_50l, sonde, splits, temperature, time, vol, width";
String license "https://www.bco-dmo.org/dataset/746107/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/746107";
Float64 Northernmost_Northing 29.6996;
String param_mapping "{'746107': {'lat': 'master - latitude', 'depth': 'master - depth', 'lon': 'master - longitude', 'ISO_DateTime_UTC': 'master - time'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/746107/parameters";
String people_0_affiliation "University of Maryland Center for Environmental Science";
String people_0_affiliation_acronym "UMCES/HPL";
String people_0_person_name "Michael R. Roman";
String people_0_person_nid "50513";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of Maryland Center for Environmental Science";
String people_1_affiliation_acronym "UMCES/HPL";
String people_1_person_name "Klaus B. Huebert";
String people_1_person_nid "746092";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "East Carolina University";
String people_2_affiliation_acronym "ECU-ICSP";
String people_2_person_name "David G. Kimmel";
String people_2_person_nid "51377";
String people_2_role "Co-Principal Investigator";
String people_2_role_type "originator";
String people_3_affiliation "University of Maryland Center for Environmental Science";
String people_3_affiliation_acronym "UMCES/HPL";
String people_3_person_name "James J. Pierson";
String people_3_person_nid "51109";
String people_3_role "Co-Principal Investigator";
String people_3_role_type "originator";
String people_4_affiliation "University of Maryland Center for Environmental Science";
String people_4_affiliation_acronym "UMCES/HPL";
String people_4_person_name "Klaus B. Huebert";
String people_4_person_nid "746092";
String people_4_role "Contact";
String people_4_role_type "related";
String people_5_affiliation "Woods Hole Oceanographic Institution";
String people_5_affiliation_acronym "WHOI BCO-DMO";
String people_5_person_name "Amber York";
String people_5_person_nid "643627";
String people_5_role "BCO-DMO Data Manager";
String people_5_role_type "related";
String project "GoMX - NGOMEX";
String projects_0_acronym "GoMX - NGOMEX";
String projects_0_description
"NGOMEX - Living Organisms of the Northern Gulf of Mexico
A synthesis of data collected in the Northern Gulf of Mexico from 2003-2004, 2006-2008 and 2010
Data include:
- CTD Profiles
- Rosette Samples
- MIDAS underway metereological
- Towed SCANFISH
- Net Trawls
- Zooplankton counts
High-resolution mapping of the major ecosystem components of the NGOMEX by year
References:
Kimmel, D. G., W. C. Boicourt, J. J. Pierson, M. R. Roman, X. Zhang. 2010. The vertical distribution and diel variability of mesozooplankton biomass, abundance and size in response to hypoxia in the northern Gulf of Mexico USA. Journal of Plankton Research 32(8): 1185-1202. doi:10.1093/plankt/fbp136
Pierson, J. J., M. R. Roman, D. G. Kimmel, W. C. Boicourt, & X. Zhang. 2009. Quantifying changes in the vertical distribution of mesozooplankton in response to hypoxic bottom waters. Journal of Experimental Marine Biology and Ecology 381: S74-S79. doi.org/10.1016/j.jembe.2009.07.013
Kimmel, D. G., W. C. Boicourt, J. J. Pierson, M. R. Roman, & X. Zhang. 2009. A comparison of the mesozooplankton response to hypoxia in Chesapeake Bay and the northern Gulf of Mexico using the biomass size spectrum. Journal of Experimental Marine Biology and Ecology 381: S65-S73. doi.org/10.1016/j.jembe.2009.07.012
Zhang, H., S. A. Ludsin, D. M. Mason, A. T. Adamack, S. B. Brandt, X. Zhang, D. G. Kimmel, M. R. Roman, & W. C. Boicourt. 2009. Hypoxia-driven changes in the behavior and spatial distribution of pelagic fish and mesozooplankton in the northern Gulf of Mexico. Journal of Experimental Marine Biology and Ecology. 381: S80-91. https://dx.doi.org/10.1016/j.jembe.2009.07.014";
String projects_0_geolocation "Northern Gulf of Mexico, 28-30N 89-94W";
String projects_0_name "NGOMEX - Living Marine Resources of the Northern Gulf of Mexico";
String projects_0_project_nid "2123";
String projects_0_start_date "2003-01";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 28.39068;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "CTD casts using a high-capacity, diaphragm pump were conducted during the R/V Pelican cruises PE03-NGOMEX, PE04-NGOMEX, PE06-NGOMEX, PE07-NGOMEX, and PE09-05 in the Northern Gulf of Mexico between 2003 and 2008. Plankton samples were collected from discrete depths during the CTD casts. Subsamples of sample contents were manually counted, identified, and measured in the laboratory.";
String time_coverage_end "2008-08-12T02:19:04Z";
String time_coverage_start "2003-07-30T17:07:15Z";
String title "[Pump mesozooplankton samples] - Mesozooplankton sample data from R/V Pelican cruises PE03-NGOMEX, PE04-NGOMEX, PE06-NGOMEX, PE07-NGOMEX, PE09-05 in the Northern Gulf of Mexico from 2003-2008 (NGOMEX - Living Marine Resources of the Northern Gulf of Mexico)";
String version "2";
Float64 Westernmost_Easting -93.65449;
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.