Accessing BCO-DMO data
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| Dataset Title: | [Palau Environmental: 2010] - Environmental data collected in marine lakes in Palau in 2010 from small boats (Do Parallel Patterns Arise from Parallel Processes?) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_683072) |
| Information: | Summary
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Attributes {
s {
sample {
String bcodmo_name "sample";
String description "Sample identifier";
String long_name "Sample";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
lake {
String bcodmo_name "site";
String description "Lake name";
String long_name "Lake";
String units "unitless";
}
date {
String bcodmo_name "date";
String description "Date sampled, formatted as yyyy-mm-dd";
String long_name "Date";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String source_name "date";
String time_precision "1970-01-01";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 7.1165, 7.32285;
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 134.2693667, 134.50855;
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";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 0.0, 30.0;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "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";
}
temp {
Float32 _FillValue NaN;
Float32 actual_range 28.8, 32.5;
String bcodmo_name "temperature";
String description "Temperature";
String long_name "Temperature";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/";
String units "degrees Celsius";
}
cond {
Float32 _FillValue NaN;
Float32 actual_range 33.7, 51.1;
String bcodmo_name "conductivity";
String description "Conductivity";
String long_name "Cond";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/CNDC/";
String units "milliSiemens per centimeter (mS/cm)";
}
sal {
Float32 _FillValue NaN;
Float32 actual_range 21.4, 34.0;
String bcodmo_name "sal";
String description "Salinity";
String long_name "Sal";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/";
String units "ppt";
}
O2_diss {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 203.0;
String bcodmo_name "dissolved Oxygen";
String description "Dissolved oxygen";
String long_name "O2 Diss";
String units "micromolar (uM)";
}
pH {
Float32 _FillValue NaN;
Float32 actual_range 6.83, 8.12;
String bcodmo_name "pH";
Float64 colorBarMaximum 9.0;
Float64 colorBarMinimum 7.0;
String description "pH";
String long_name "Sea Water Ph Reported On Total Scale";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/";
String units "unitless";
}
chl {
Float32 _FillValue NaN;
Float32 actual_range 3.42, 256.03;
String bcodmo_name "unknown";
String description "Chlorophyll";
String long_name "CHL";
String units "micrograms per liter (ug/L)";
}
phosphate {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 11.0;
String bcodmo_name "PO4";
String description "Phosphate";
String long_name "Mass Concentration Of Phosphate In Sea Water";
String units "micromolar (uM)";
}
nitrite {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.42;
String bcodmo_name "NO2";
Float64 colorBarMaximum 1.0;
Float64 colorBarMinimum 0.0;
String description "Nitrite";
String long_name "Mole Concentration Of Nitrite In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRIAAZX/";
String units "micromolar (uM)";
}
ammonium {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 268.0;
String bcodmo_name "Ammonium";
Float64 colorBarMaximum 5.0;
Float64 colorBarMinimum 0.0;
String description "Ammonium";
String long_name "Mole Concentration Of Ammonium In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AMONAAZX/";
String units "micromolar (uM)";
}
nitrate {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.83;
String bcodmo_name "NO3";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Nitrate";
String long_name "Mole Concentration Of Nitrate In Sea Water";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/NTRAIGGS/";
String units "micromolar (uM)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Refer to the following paper for complete methodology:
Meyerhof, M. et al. 2016.\\u00a0Microbial community diversity, structure and
assembly across oxygen gradients in meromictic marine lakes, Palau.
Environmental Microbiology.
doi:[10.1111/1462-2920.13416](\\\\\"https://dx.doi.org/10.1111/1462-2920.13416\\\\\")
In summary (extracted from above paper):
We studied five meromictic lakes in Palau: Spooky Lake (SLM), Goby Lake
(GLK), Ongeim\\u2019l Tketau Lake (OTM, known colloquially as Jellyfish Lake),
Clear Lake (CLM) and Ngermeuangel Lake (NLK). One holomictic lake (Mekeald
Lake; MLN) and an ocean site at the German Channel on the southwestern side of
the islands (OS-GC) were also sampled for comparison. We vertically profiled
dissolved oxygen (DO), temperature, pH, chlorophyll fluorescence and
salinity/conductivity using a HydroLab DS5 (Hach Company, Loveland, CO, USA)
and sampled three depth layers within each meromictic lake: the mixolimnion
(0\\u20135 m depth), the monimolimnion (5\\u201320 m depth) and intermediate
depths near the chemocline; these intermediate depths ranged from 1 to 15 m,
depending on the depth of the chemocline within the individual lakes. We
sampled comparable depths at MLN (5\\u201320 m) and OS-GC (5\\u201330 m). For
QPCR analysis of functional genes (dsrA, amoA and nirS) and specific
functional groups, as well as analysis dissolved nutrient concentrations, we
collected additional samples above and below the chemocline to capture abrupt
transitions in biogeochemical conditions across this interface.
Samples were collected from small boats using a horizontal, 2.5 L GoFlo bottle
(General Oceanics, Miami, FL, USA), transferred to 1 L polycarbonate bottles,
and stored in the dark during transit to the Coral Reef Research Foundation
laboratory in Koror, Palau. Water samples were filtered using a peristaltic
pump and 0.22 um Durapore PVDF hydrophilic filters (Millipore, Billerica, MA,
USA). Filters were immediately frozen in 800 uL Sucrose-Tris-EDTA (STE) lysis
buffer (750 mM sucrose, 20 mM EDTA, 400 mM NaCl and 50 mM Tris) in 2 mL Lysing
Matrix E tubes (MP Biomedicals, Solon, OH, USA), and stored at -20 C until
transport to the United States, where they were stored at -80 C until
extraction (Dry ice and liquid nitrogen are not readily available in Palau.)
During sample filtration, 50 mL of filtrate was collected in high density
polyethylene bottles for subsequent nutrient analysis at the University of
California, Santa Barbara (UCSB) Marine Analytical Laboratory. Samples were
analyzed for ammonium (UCSB MAL analytical method for ammonium, see below;
Diamond and Huberty, 1996), nitrite (Environmental Protection Agency (EPA)
Method 353.2; Schroeder, 1997), nitrite+nitrate (EPA Method 353.2; Diamond,
1997) and phosphate (EPA Method 365.1; Huberty and Diamond, 1998), on a Lachat
QuikChem 8000 Flow Injection Analyzer (Hach Company, Loveland, CO, USA). A
handful of samples containing large concentrations of sulfide were not
analyzed for nitrate, as sulfide damages the cadmium reduction column. For
ammonium analysis, each sample was injected into a flowing carrier stream
through an injection valve, and then merged with an alkaline solution stream;
the produced ammonia was diffused through a hydrophobic, gas-permeable
membrane into a recipient stream containing a pH indicator. Colour change
occurs in the indicator solution due to an increase in pH, and the
concentration of ammonia was determined spectrophotometrically based on
absorption at 570 nm. For all analyses, a mid-range check standard bracketed
every 20 samples to verify the accuracy of the measurements, and samples that
were detected outside of the standards\\u2019 range were diluted 1:10 and
reanalyzed. Detection limits were 0.10 uM for phosphate, 0.10 uM for nitrite,
0.20 uM for nitrite+nitrate and 0.10 uM for ammonium.";
String awards_0_award_nid "55103";
String awards_0_award_number "OCE-1241255";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1241255";
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
"Palau 2010 Environmental Data
PI: Michael Beman (UC Merced)
Co-PI: Michael Dawson (UC Merced)
Version: 24 February 2017";
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 "2017-02-24T21:37:03Z";
String date_modified "2019-08-05T16:48:19Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.683072.1";
Float64 Easternmost_Easting 134.50855;
Float64 geospatial_lat_max 7.32285;
Float64 geospatial_lat_min 7.1165;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max 134.50855;
Float64 geospatial_lon_min 134.2693667;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 30.0;
Float64 geospatial_vertical_min 0.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-12-21T15:43:50Z (local files)
2024-12-21T15:43:50Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_683072.html";
String infoUrl "https://www.bco-dmo.org/dataset/683072";
String institution "BCO-DMO";
String instruments_0_acronym "GO-FLO";
String instruments_0_dataset_instrument_description "Samples were collected from small boats using a horizontal, 2.5 L GoFlo bottle (General Oceanics, Miami, FL, USA).";
String instruments_0_dataset_instrument_nid "683390";
String instruments_0_description "GO-FLO bottle cast used to collect water samples for pigment, nutrient, plankton, etc. The GO-FLO sampling bottle is specially designed to avoid sample contamination at the surface, internal spring contamination, loss of sample on deck (internal seals), and exchange of water from different depths.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/30/";
String instruments_0_instrument_name "GO-FLO Bottle";
String instruments_0_instrument_nid "411";
String instruments_0_supplied_name "GoFlo bottle";
String instruments_1_acronym "FIA";
String instruments_1_dataset_instrument_description "Samples were analyzed for ammonium, nitrite, nitrite+nitrate, and phosphate on a Lachat QuikChem 8000 Flow Injection Analyzer (Hach Company, Loveland, CO, USA).";
String instruments_1_dataset_instrument_nid "683391";
String instruments_1_description "An instrument that performs flow injection analysis. Flow injection analysis (FIA) is an approach to chemical analysis that is accomplished by injecting a plug of sample into a flowing carrier stream. FIA is an automated method in which a sample is injected into a continuous flow of a carrier solution that mixes with other continuously flowing solutions before reaching a detector. Precision is dramatically increased when FIA is used instead of manual injections and as a result very specific FIA systems have been developed for a wide array of analytical techniques.";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB36/";
String instruments_1_instrument_name "Flow Injection Analyzer";
String instruments_1_instrument_nid "657";
String instruments_1_supplied_name "Lachat QuikChem 8000 Flow Injection Analyzer";
String instruments_2_acronym "HydroLab DS5";
String instruments_2_dataset_instrument_description "Dissolved oxygen (DO), temperature, pH, chlorophyll fluorescence and salinity/conductivity were measured using a HydroLab DS5 Multiparameter Data Sonde (Hach Company, Loveland, CO, USA).";
String instruments_2_dataset_instrument_nid "683389";
String instruments_2_description "Multi-parameter probes that can measure from 12 (MS5) to 16 (DS5 and DS5X) parameters simultaneously. Measurements include temperature, depth, conductivity, salinity, specific conductance, TDS, pH, ORP, dissolved oxygen, turbidity, chlorophyll a, blue-green algae, Rhodamine WT, ammonium, nitrate, chloride, PAR and total dissolved gases. These probes can be deployed at depths up to 200 m and can be used in continuous monitoring programs.";
String instruments_2_instrument_name "Hydrolab Series 5 probes";
String instruments_2_instrument_nid "768060";
String instruments_2_supplied_name "HydroLab DS5";
String keywords "altimetry, ammonia, ammonium, bco, bco-dmo, biological, chemical, chemistry, chl, chlorophyll, concentration, cond, data, dataset, date, depth, diss, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Nitrate, Earth Science > Oceans > Ocean Chemistry > pH, Earth Science > Oceans > Ocean Chemistry > Phosphate, erddap, laboratory, lake, latitude, longitude, management, mass, mass_concentration_of_phosphate_in_sea_water, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_nitrate_in_sea_water, mole_concentration_of_nitrite_in_sea_water, n02, nh4, nitrate, nitrite, no3, O2, O2_diss, ocean, oceanography, oceans, office, oxygen, phosphate, po4, preliminary, reported, sal, sample, satellite, scale, science, sea, sea_water_ph_reported_on_total_scale, seawater, temperature, time, total, water";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/683072/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/683072";
Float64 Northernmost_Northing 7.32285;
String param_mapping "{'683072': {'lat': 'master - latitude', 'depth': 'master - depth', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/683072/parameters";
String people_0_affiliation "University of California-Merced";
String people_0_affiliation_acronym "UC Merced";
String people_0_person_name "John Michael Beman";
String people_0_person_nid "51552";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of California-Merced";
String people_1_affiliation_acronym "UC Merced";
String people_1_person_name "Michael N Dawson";
String people_1_person_nid "51577";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "University of California-Merced";
String people_2_affiliation_acronym "UC Merced";
String people_2_person_name "John Michael Beman";
String people_2_person_nid "51552";
String people_2_role "Contact";
String people_2_role_type "related";
String people_3_affiliation "Woods Hole Oceanographic Institution";
String people_3_affiliation_acronym "WHOI BCO-DMO";
String people_3_person_name "Shannon Rauch";
String people_3_person_nid "51498";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "PaPaPro";
String projects_0_acronym "PaPaPro";
String projects_0_description
"This project will survey the taxonomic, genetic, and functional diversity of the organisms found in marine lakes, and investigate the processes that cause gains and losses in this biodiversity. Marine lakes formed as melting ice sheets raised sea level after the last glacial maximum and flooded hundreds of inland valleys around the world. Inoculated with marine life from the surrounding sea and then isolated to varying degrees for the next 6,000 to 15,000 years, these marine lakes provide multiple, independent examples of how environments and interactions between species can drive extinction and speciation. Researchers will survey the microbes, algae, invertebrates, and fishes present in 40 marine lakes in Palau and Papua, and study how diversity has changed over time by retrieving the remains of organisms preserved in sediments on the lake bottoms. The project will test whether the number of species, the diversity of functional roles played by organisms, and the genetic diversity within species increase and decrease in parallel; whether certain species can greatly curtail diversity by changing the environment; whether the size of a lake determines its biodiversity; and whether the processes that control diversity in marine organisms are similar to those that operate on land.
Because biodiversity underlies the ecosystem services on which society depends, society has a great interest in understanding the processes that generate and retain biodiversity in nature. This project will also help conserve areas of economic importance. Marine lakes in the study region are important for tourism, and researchers will work closely with governmental and non-governmental conservation and education groups and with diving and tourism businesses to raise awareness of the value and threats to marine lakes in Indonesia and Palau.";
String projects_0_end_date "2017-12";
String projects_0_geolocation "Western Pacific; Palau; Indonesia (West Papua)";
String projects_0_name "Do Parallel Patterns Arise from Parallel Processes?";
String projects_0_project_nid "2238";
String projects_0_project_website "http://marinelakes.ucmerced.edu/";
String projects_0_start_date "2013-01";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 7.1165;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Environmental data collected in marine lakes in Palau in 2010 from small boats. Reported parameters include depth, temperature, conductivity, salinity, oxygen, pH, light, chlorophyll, phosphate, nitrite, ammonium, and nitrate.";
String title "[Palau Environmental: 2010] - Environmental data collected in marine lakes in Palau in 2010 from small boats (Do Parallel Patterns Arise from Parallel Processes?)";
String version "1";
Float64 Westernmost_Easting 134.2693667;
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.