Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | [IrnBru MV1405 - FvFm and Lifetime Fluorescence] - FvFm and fluorescence lifetime data collected from the R/V Melville MV1405 along the California Coastline during 2014 (Linking physiological and molecular aspects of diatom silicification in field populations) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_652298) |
| Information: | Summary
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| FGDC
| ISO 19115
| Metadata
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Attributes {
s {
cruise_id {
String bcodmo_name "cruise_id";
String description "cruise identification";
String long_name "Cruise Id";
String units "unitless";
}
date_gmt {
String bcodmo_name "date_gmt";
String description "GMT date; mm/dd/yy";
String long_name "Date Gmt";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 32.81, 42.88;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "latitude";
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 -127.32, -117.62;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "longitude";
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";
}
time_gmt {
String bcodmo_name "time_gmt";
String description "GMT time; HH:MM";
String long_name "Time Gmt";
String units "unitless";
}
corr_Fluor_min {
Float32 _FillValue NaN;
Float32 actual_range 63.36, 12996.48;
String bcodmo_name "fluorescence";
String description "minimal fluorescence yield corrected for background fluorescence by subtracting respective value measured in 0.2 micrometers filtered seawater from sample data";
String long_name "Corr Fluor Min";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLPM01/";
String units "relative units";
}
corr_Fluor_max {
Float32 _FillValue NaN;
Float32 actual_range 116.62, 29651.86;
String bcodmo_name "fluorescence";
String description "maximal fluorescence yield corrected for background fluorescence by subtracting respective value measured in 0.2 micrometers filtered seawater from sample data";
String long_name "Corr Fluor Max";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLPM01/";
String units "relative units";
}
corr_FvFm {
Float32 _FillValue NaN;
Float32 actual_range 0.039, 0.64;
String bcodmo_name "Fv2Fm";
String description "maximum photosynthetic efficiency of photosystem II (quantum yield of photochemistry)";
String long_name "Corr Fv Fm";
String units "dimensionless";
}
functional_absorbtion {
Int16 _FillValue 32767;
Int16 actual_range 68, 5594;
String bcodmo_name "unknown";
String description "sigma; functional absorption cross-section of photosystem II (PSII)";
String long_name "Functional Absorbtion";
String units "unitless";
}
NPQ {
Float32 _FillValue NaN;
Float32 actual_range -0.198, 2.208;
String bcodmo_name "unknown";
String description "non-photochemical quenching";
String long_name "NPQ";
String units "dimensionless";
}
amp1 {
Float32 _FillValue NaN;
Float32 actual_range 0.02, 0.966;
String bcodmo_name "unknown";
String description "amplitude 1 of the different components of the deconvolution of the fluorescence lifetime kinetics";
String long_name "Amp1";
String units "dimensionless";
}
amp2 {
Float32 _FillValue NaN;
Float32 actual_range 0.02, 0.98;
String bcodmo_name "unknown";
String description "amplitude 2 of the different components of the deconvolution of the fluorescence lifetime kinetics";
String long_name "Amp2";
String units "dimensionless";
}
amp3 {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.898;
String bcodmo_name "unknown";
String description "amplitude 3 of the different components of the deconvolution of the fluorescence lifetime kinetics";
String long_name "Amp3";
String units "dimensionless";
}
time1 {
Float32 _FillValue NaN;
Float32 actual_range 0.02, 1.411;
String bcodmo_name "time_elapsed";
String description "time 1 of the different components of the fluorescence lifetime kinetics";
String long_name "Time1";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
String units "picosecond";
}
time2 {
Float32 _FillValue NaN;
Float32 actual_range 0.022, 2.488;
String bcodmo_name "time_elapsed";
String description "time 2 of the different components of the fluorescence lifetime kinetics";
String long_name "Time2";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
String units "picosecond";
}
time3 {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 2.495;
String bcodmo_name "time_elapsed";
String description "time 3 of the different components of the fluorescence lifetime kinetics";
String long_name "Time3";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/";
String units "picosecond";
}
TAV {
Float32 _FillValue NaN;
Float32 actual_range 0.5, 2.347;
String bcodmo_name "mean";
String description "average lifetime of fluorescence";
String long_name "TAV";
String units "picosecond";
}
time {
String _CoordinateAxisType "Time";
Float64 actual_range 1.40442576e+9, 1.4063244e+9;
String axis "T";
String bcodmo_name "ISO_DateTime_UTC";
String description "DateTime (UTC) ISO formatted";
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";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
String acquisition_description
"A custom-built Fast Repetition Rate Fluorometer and Lifetime Fluorometer
measured surface water continuously using the ship's underway water system.
Background fluorescence was measured daily using 0.2 um filtered seawater and
manually subtracted from sample data.\\u00a0";
String awards_0_award_nid "558197";
String awards_0_award_number "OCE-1333929";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1333929";
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 "558203";
String awards_1_award_number "OCE-1334387";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1334387";
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 cdm_data_type "Other";
String comment
"FvFm and Lifetime Fluorescence
K. Thamatrakoln and M. Brzezinski, PIs
FvFm and lifetime fluorescence from the MV1405 cruise.
NPQ = non-photochemical quenching";
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 "2016-07-21T18:49:16Z";
String date_modified "2020-01-29T17:56:06Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.652298.1";
Float64 Easternmost_Easting -117.62;
Float64 geospatial_lat_max 42.88;
Float64 geospatial_lat_min 32.81;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -117.62;
Float64 geospatial_lon_min -127.32;
String geospatial_lon_units "degrees_east";
String history
"2024-11-23T17:22:03Z (local files)
2024-11-23T17:22:03Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_652298.html";
String infoUrl "https://www.bco-dmo.org/dataset/652298";
String institution "BCO-DMO";
String instruments_0_acronym "FRRf";
String instruments_0_dataset_instrument_description "A custom-built Fast Repetition Rate Fluorometer continuously measured surface water using the ships underway water system.";
String instruments_0_dataset_instrument_nid "652310";
String instruments_0_description "An FRRf is used for measuring the fluorescence of a sample of phytoplankton photosynthetic competency (Fv/Fm).";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/113/";
String instruments_0_instrument_name "Fast Repetition Rate Fluorometer";
String instruments_0_instrument_nid "426";
String instruments_0_supplied_name "Fast Repetition Rate Fluorometer";
String instruments_1_acronym "Lifetime Fluorometer";
String instruments_1_dataset_instrument_description "A custom-built Lifetime Fluorometer continuously measured surface water using the ships underway water system.";
String instruments_1_dataset_instrument_nid "652861";
String instruments_1_description "A Lifetime Fluorometer is used to measure picosecond fluorescence decay kinetics in phytoplankton.";
String instruments_1_instrument_name "Lifetime Fluorometer";
String instruments_1_instrument_nid "652860";
String instruments_1_supplied_name "Lifetime Fluorometer";
String keywords "absorbtion, amp1, amp2, amp3, bco, bco-dmo, biological, chemical, corr, corr_Fluor_max, corr_Fluor_min, corr_FvFm, cruise, cruise_id, data, dataset, date, date_gmt, dmo, erddap, fluor, functional, functional_absorbtion, iso, latitude, longitude, management, max, min, npq, oceanography, office, preliminary, tav, time, time1, time2, time3, time_gmt";
String license "https://www.bco-dmo.org/dataset/652298/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/652298";
Float64 Northernmost_Northing 42.88;
String param_mapping "{'652298': {'lat': 'master - latitude', 'lon': 'master - longitude', 'ISO_DateTime_UTC': 'flag - time'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/652298/parameters";
String people_0_affiliation "Rutgers University";
String people_0_affiliation_acronym "Rutgers IMCS";
String people_0_person_name "Kimberlee Thamatrakoln";
String people_0_person_nid "558200";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of California-Santa Barbara";
String people_1_affiliation_acronym "UCSB-LifeSci";
String people_1_person_name "Mark A. Brzezinski";
String people_1_person_nid "50663";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Rutgers University";
String people_2_person_name "Dr Maxim Gorbunov";
String people_2_person_nid "652863";
String people_2_role "Scientist";
String people_2_role_type "originator";
String people_3_affiliation "Rutgers University";
String people_3_person_name "Dr Fedor Kuzminov";
String people_3_person_nid "652862";
String people_3_role "Scientist";
String people_3_role_type "originator";
String people_4_affiliation "Rutgers University";
String people_4_affiliation_acronym "Rutgers IMCS";
String people_4_person_name "Kimberlee Thamatrakoln";
String people_4_person_nid "558200";
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 "Hannah Ake";
String people_5_person_nid "650173";
String people_5_role "BCO-DMO Data Manager";
String people_5_role_type "related";
String project "Diatom Silicification";
String projects_0_acronym "Diatom Silicification";
String projects_0_description
"Description from NSF award abstract:
Diatoms, unicellular, eukaryotic photoautotrophs, are among the most ecologically successful and functionally diverse organisms in the ocean. In addition to contributing one-fifth of total global primary productivity, diatoms are also the largest group of silicifying organisms in the ocean. Thus, diatoms form a critical link between the carbon and silicon (Si) cycles. The goal of this project is to understand the molecular regulation of silicification processes in natural diatom populations to better understand the processes controlling diatom productivity in the sea. Through culture studies and two research cruises, this research will couple classical measurements of silicon uptake and silica production with molecular and biochemical analyses of Silicification-Related Gene (SiRG) and protein expression. The proposed cruise track off the West Coast of the US will target gradients in Si and iron (Fe) concentrations with the following goals: 1) Characterize the expression pattern of SiRGs, 2) Correlate SiRG expression patterns to Si concentrations, silicon uptake kinetics, and silica production rates, 3) Develop a method to normalize uptake kinetics and silica production to SiRG expression levels as a more accurate measure of diatom activity and growth, 4) Characterize the diel periodicity of silica production and SiRG expression.
It is estimated that diatoms process 240 Teramoles of biogenic silica each year and that each molecule of silicon is cycled through a diatom 39 times before being exported to the deep ocean. Decades of oceanographic and field research have provided detailed insight into the dynamics of silicon uptake and silica production in natural populations, but a molecular understanding of the factors that influence silicification processes is required for further understanding the regulation of silicon and carbon fluxes in the ocean. Characterizing the genetic potential for silicification will provide new information on the factors that regulate the distribution of diatoms and influence in situ rates of silicon uptake and silica production. This research is expected to provide significant information about the molecular regulation of silicification in natural populations and the physiological basis of Si limitation in the sea.";
String projects_0_end_date "2016-08";
String projects_0_geolocation "Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W";
String projects_0_name "Linking physiological and molecular aspects of diatom silicification in field populations";
String projects_0_project_nid "558198";
String projects_0_start_date "2013-09";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 32.81;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "cruise_id";
String summary "FvFm and fluorescence lifetime data collected from the R/V Melville MV1405 along the California Coastline during 2014.";
String time_coverage_end "2014-07-25T21:40:00Z";
String time_coverage_start "2014-07-03T22:16:00Z";
String title "[IrnBru MV1405 - FvFm and Lifetime Fluorescence] - FvFm and fluorescence lifetime data collected from the R/V Melville MV1405 along the California Coastline during 2014 (Linking physiological and molecular aspects of diatom silicification in field populations)";
String version "1";
Float64 Westernmost_Easting -127.32;
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.