Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | [bacteria_FCM_lab] - Heterotrophic (non-pigmented) bacteria abundances determined by flow cytometry (post-cruise/on-shore analysis) 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_516204) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
event {
Int16 _FillValue 32767;
Int16 actual_range 17, 1111;
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 3, 85;
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). 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 6.6219, 10.2998;
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 -92.9871, -86.735;
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, 120.0;
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";
}
bact_het_cyt {
Int32 _FillValue 2147483647;
Int32 actual_range 22569, 1706696;
String bcodmo_name "bact_het_cyt";
String description "Heterotrophic bacteria (non-pigmented bacteria) abundance.";
String long_name "Bact Het Cyt";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/HBCCXXXX/";
String units "cells per milliliter (cells/mL)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Samples were collected from the CTD-Rosette PVC Niskin bottles, then preserved
with paraformaldehyde (0.5% final concentration). Preserved samples were then
flash frozen in liquid nitrogen, and subsequently stored at -80\\u00b0C until
analysis on-shore in batches. Upon thawing, samples were stained with Hoechst
33342 DNA stain (1 ug/mL final concentration), incubated at room temperature
in the dark for 1 h, then analyzed using a Beckman-Coulter Altra flow
cytometer, equipped with one 488 nm 1W laser and one UV 200 mM laser for
excitation. Samples (100 ul) were delivered quantitatively to the instrument
using a Harvard Apparatus syringe pump, at a rate of 50 ul per minute. Signals
from the DNA detector (450\\u00b140 nm) and the forward and side scatter
detectors were used to delineate non-pigmented bacteria, in conjunction with
the Chlorophyll detector (680\\u00b120 nm) and Phycoerythrin detector
(575\\u00b120 nm) to eliminate chlorophyll and/or phycoerythrin-bearing cells
that overlapped (e.g., Prochlorococcus and Synechoccoccus). Calibration beads
(0.5 u\\u00b5m and 1.0 um yellow-green and 0.5 um UV) were used to normalize
cellular fluorescence values and assure optimal instrument settings. Raw data
files (listmode) were processed in FlowJo software (Treestar Inc.).";
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 (non-pigmented) bacteria abundance (on-shore analysis)
PI: Michael Landry (UCSD-SIO)
Contact: Karen Selph (UH)
Version: 30 May 2014";
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 "2014-05-30T17:19:48Z";
String date_modified "2019-12-11T19:57:15Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.516204.1";
Float64 Easternmost_Easting -86.735;
Float64 geospatial_lat_max 10.2998;
Float64 geospatial_lat_min 6.6219;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -86.735;
Float64 geospatial_lon_min -92.9871;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 120.0;
Float64 geospatial_vertical_min 2.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-21T08:46:29Z (local files)
2024-11-21T08:46:29Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_516204.html";
String infoUrl "https://www.bco-dmo.org/dataset/516204";
String institution "BCO-DMO";
String instruments_0_acronym "Niskin bottle";
String instruments_0_dataset_instrument_description "Samples were collected from the CTD-Rosette PVC Niskin bottles.";
String instruments_0_dataset_instrument_nid "516233";
String instruments_0_description "A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24 or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/";
String instruments_0_instrument_name "Niskin bottle";
String instruments_0_instrument_nid "413";
String instruments_0_supplied_name "Niskin bottle";
String instruments_1_acronym "Flow Cytometer";
String instruments_1_dataset_instrument_description "Samples were run on a Beckman-Coulter Altra flow cytometer, equipped with one 488 nm 1W laser and one UV 200 mM laser for excitation.";
String instruments_1_dataset_instrument_nid "516232";
String instruments_1_description
"Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB37/";
String instruments_1_instrument_name "Flow Cytometer";
String instruments_1_instrument_nid "660";
String instruments_1_supplied_name "Beckman-Coulter Altra flow cytometer";
String keywords "bact, bact_het_cyt, bco, bco-dmo, biological, cast, chemical, cycle, cyt, data, dataset, date, date_local, depth, dmo, erddap, event, het, latitude, local, longitude, management, niskin, oceanography, office, preliminary";
String license "https://www.bco-dmo.org/dataset/516204/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/516204";
Float64 Northernmost_Northing 10.2998;
String param_mapping "{'516204': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/516204/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 Hawaii at Manoa";
String people_1_affiliation_acronym "SOEST";
String people_1_person_name "Karen Selph";
String people_1_person_nid "50848";
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 6.6219;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Non-pigmented bacteria abundances from preserved (0.5% paraformaldehyde) frozen samples run on a Beckman-Coulter Altra flow cytometer after staining with Hoechst 33342 DNA stain and excitation with 200 mW UV and 1W 488 nm laser light. Bacteria discriminated based on DNA content (450\\u00b140 nm), as well as forward and 90\\u00b0 side light scatter parameters. Samples were collected on the MV1008 cruise in the Costa Rica Dome (CRD) region of the Eastern Tropical Pacific Ocean.";
String title "[bacteria_FCM_lab] - Heterotrophic (non-pigmented) bacteria abundances determined by flow cytometry (post-cruise/on-shore analysis) 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 -92.9871;
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.