Accessing BCO-DMO data
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| Dataset Title: | [microzoo_epi_biomass] - Carbon biomass estimates of heterotrophic protists by size-class, based on epifluorescence microscopy from samples collected on R/V Melville cruise MV1008 in the Costa Rica Dome in 2010 (CRD FLUZiE project) (Costa Rica Dome FLUx and Zinc Experiments) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_517455) |
| Information: | Summary
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| FGDC
| ISO 19115
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Attributes {
s {
event {
Int16 _FillValue 32767;
Int16 actual_range 304, 950;
String bcodmo_name "event";
String description "Number referring to the particular activity (event) on the FluZiE cruise.";
String long_name "Event";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/EVTAGFL/";
String units "integer";
}
cast {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 25, 70;
String bcodmo_name "cast";
String description "CTD Cast number from the FluZiE cruise.";
String long_name "Cast";
String units "integer";
}
cycle {
String bcodmo_name "unknown";
String description "Type and number of cruise sampling event. Either \"Stn_n\" or \"Cycle_n\". A transect of stations was sampled from 29 June to 03 July. Five quasi-Lagrangian experiments called \"cycles\" were conducted during the remainder of the cruise.";
String long_name "Cycle";
String units "text";
}
date_local {
String bcodmo_name "date";
String description "Date of CTD cast (local time zone of UTC -6). in the format mmddyyyy";
String long_name "Date Local";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 8.39218, 10.29979;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude in degrees North.";
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";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -92.98714, -89.99424;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude in degrees East.";
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";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 2.0, 100.0;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Sample 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";
}
niskin {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 22;
String bcodmo_name "bot_Nis";
String description "Niskin bottle that the sample was taken from.";
String long_name "Niskin";
String units "integer";
}
taxon {
String bcodmo_name "taxon";
String description "Taxon. heterotrophic_dinos = Heterotrophic Dinoflagellates; heterotrophic_flags = Heterotrophic Flagellates; all = all taxonomic groups (heterotrophic dinoflagellates + heterotrophic flagellates)";
String long_name "Taxon";
String units "text";
}
size_class {
String bcodmo_name "unknown";
String description "Size-Class Distribution (cell lengths are longest major axis): lt2 = cells < 2 um; 2_to_10 = cells 2-10 um; 10_to_20 = cells 10-20 um; gt20 = cells > 20 um; total = all sizes.";
String long_name "Size Class";
String units "micrometers (um)";
}
biomass {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 17.02;
String bcodmo_name "biomass_C";
String description "Carbon biomass of the taxon size class.";
String long_name "Biomass";
String units "micrograms Carbon per liter (ug C L-1)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Seawater samples (500 mL) for microscopical analysis were gently collected
from the CTD and immediately preserved for slide preparation according to a
modified protocol of Sherr and Sherr (1993). The samples were first preserved
with 260 uL of alkaline Lugol\\u2019s solution, immediately followed by 10 mL
of buffered formalin and 500 uL of sodium thiosulfate, with gentle mixing
between each addition. Preserved samples were shielded from light and left to
rest at room temperature for 1 h. After the rest period, 1 mL of proflavin
(0.33% w/v) was added and the samples were stored in the dark for an
additional hour. Just prior to filtration, the preserved samples were stained
with 1 mL of DAPI (0.01 mg mL-1) and immediately transferred to the filtration
manifold. A 50-mL aliquot (small volume, SV) of the sample was filtered
through a 25-mm black polycarbonate filter with 0.8-um pore size, and the
remaining 450 mL aliquot (large volume, LV) was filtered through a 25-mm black
polycarbonate filter with 8.0-um pores. A 10-mm nylon backing filter was
placed under all polycarbonate filters to promote even cell distribution, and
filtered the samples under gentle vacuum pressure (<100 mm Hg). Each filter
was then mounted onto glass slides with one drop of Type DF immersion oil and
a No. 2 cover slip, and the prepared slides were frozen at -80\\u00b0C for
later analysis in the lab. NOTE: ciliated protists are poorly preserved by
this method and are not included in these analyses.";
String awards_0_award_nid "515386";
String awards_0_award_number "OCE-0826626";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0826626";
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
"Heterotrophic Protist Carbon Biomass (by epifluorescence microscopy)
PI: Michael Landry (UCSD-SIO)
Contact: Andrew Taylor (UCSD-SIO)
Version: 24 June 2014
Note: size_class: lt2 = less than 2 um; gt20 = greater than 20 um.";
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 "2014-06-24T19:31:20Z";
String date_modified "2019-12-30T15:31:05Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.517455.1";
Float64 Easternmost_Easting -89.99424;
Float64 geospatial_lat_max 10.29979;
Float64 geospatial_lat_min 8.39218;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -89.99424;
Float64 geospatial_lon_min -92.98714;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 100.0;
Float64 geospatial_vertical_min 2.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-05T10:29:57Z (local files)
2024-11-05T10:29:57Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_517455.html";
String infoUrl "https://www.bco-dmo.org/dataset/517455";
String institution "BCO-DMO";
String instruments_0_acronym "camera";
String instruments_0_dataset_instrument_description "Digital images were acquired with a Zeiss AxioCam MRc black and white 8-bit CCD camera.";
String instruments_0_dataset_instrument_nid "517462";
String instruments_0_description "All types of photographic equipment including stills, video, film and digital systems.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/311/";
String instruments_0_instrument_name "Camera";
String instruments_0_instrument_nid "520";
String instruments_0_supplied_name "Zeiss AxioCam MRc";
String instruments_1_acronym "Inverted Microscope";
String instruments_1_dataset_instrument_description "Slides were digitally imaged using a Zeiss Axiovert 200 M inverted compound microscope equipped for high-throughput epifluorescence microscopy with a motorized focus drive, stage, objective and filters.";
String instruments_1_dataset_instrument_nid "517463";
String instruments_1_description
"An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).
Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.
The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications.";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB05/";
String instruments_1_instrument_name "Inverted Microscope";
String instruments_1_instrument_nid "675";
String instruments_1_supplied_name "Zeiss Axiovert 200 M inverted compound microscope";
String keywords "array, array-data, bco, bco-dmo, biological, biomass, cast, chemical, class, comprehensive, cycle, data, dataset, date, date_local, depth, dmo, erddap, event, large, latitude, local, longitude, management, niskin, oceanography, office, preliminary, size, size_class, stewardship, system, taxon";
String license "https://www.bco-dmo.org/dataset/517455/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/517455";
Float64 Northernmost_Northing 10.29979;
String param_mapping "{'517455': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/517455/parameters";
String people_0_affiliation "University of California-San Diego";
String people_0_affiliation_acronym "UCSD-SIO";
String people_0_person_name "Michael R. Landry";
String people_0_person_nid "50545";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of California-San Diego";
String people_1_affiliation_acronym "UCSD-SIO";
String people_1_person_name "Andrew G. Taylor";
String people_1_person_nid "516476";
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 "CRD FLUZiE";
String projects_0_acronym "CRD FLUZiE";
String projects_0_description
"Research was aimed at improved understanding of plankton dynamics, carbon and nutrient fluxes, and potential trace element limitation in the Costa Rica Dome region of the eastern tropical Pacific. The specific science objectives of the 2010 R/V Melville cruise (MV1008) were:
1) to assess grazing and trace metal/nutrient controls on primary production and phytoplankton standing stocks;
2) to quantify carbon and elemental fluxes and export rates from the euphotic zone; and
3) to measure microbial population, processes, stable isotope abundances associated with the OMZ and nitrite maxima.
Additional information about MV1008 can be found in the cruise report (PDF).
NOTE: The original proposal and award abstract are not relevant. The project was originally funded by NSF as experimental tests of phytoplankton controls in the Arabian Sea. Piracy concerns in the region led to the cancellation of the research cruise in 2009, and a Change of Scope request was approved to focus the project on related issues in the Costa Rica Dome (CRD).
Though this project is not formally affiliated with any large program, it aligns with IMBER's emphasis on community ecology and biogeochemistry, and the OCB focus on carbon-based measurements of production, grazing and export processes.";
String projects_0_end_date "2013-12";
String projects_0_geolocation "Costa Rica Dome, Eastern Tropical Pacific Ocean";
String projects_0_name "Costa Rica Dome FLUx and Zinc Experiments";
String projects_0_project_nid "515387";
String projects_0_start_date "2009-01";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 8.39218;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Carbon biomass estimates of heterotrophic protists by size-class, based on epifluorescence microscopy. Samples were collected on the MV1008 cruise in the Costa Rica Dome (CRD) region of the Eastern Tropical Pacific Ocean.";
String title "[microzoo_epi_biomass] - Carbon biomass estimates of heterotrophic protists by size-class, based on epifluorescence microscopy from samples collected on R/V Melville cruise MV1008 in the Costa Rica Dome in 2010 (CRD FLUZiE project) (Costa Rica Dome FLUx and Zinc Experiments)";
String version "1";
Float64 Westernmost_Easting -92.98714;
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.