Accessing BCO-DMO data
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| Dataset Title: | [Carbonate data from water samples] - Water samples from CTD casts and vehicle- mounted bottles from the R/V Atlantis, R/V Ronald Brown, R/V Falkor, & E/V Nautilus in the Gulf of Mexico & Florida from 2010 to 2014 (Lophelia OA project) (Physiological and genetic responses of the deep-water coral, Lophelia pertusa, to ongoing ocean acidification in the Gulf of Mexico) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_658946) |
| Information: | Summary
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| FGDC
| ISO 19115
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Attributes {
s {
cruise_name {
String bcodmo_name "Cruise Name";
String description "Project investigator's cruise name";
String long_name "Cruise Name";
String units "unitless";
}
cruise_id {
String bcodmo_name "cruise_id";
String description "Official cruise identification";
String long_name "Cruise Id";
String units "unitless";
}
site {
String bcodmo_name "site";
String description "Site code where sample was taken; see lat/lons for exact location.";
String long_name "Site";
String units "unitless";
}
instrument {
String bcodmo_name "instrument";
String description "Instrument used to collect water samples; V (vehicle-mounted bottle) or CTD";
String long_name "Instrument";
String units "unitless";
}
measurement_location {
String bcodmo_name "sample_type";
String description "Location where water sample was taken; WC= water column or B= bottom";
String long_name "Measurement Location";
String units "unitless";
}
sample_ID {
Int16 _FillValue 32767;
Int16 actual_range 1, 243;
String bcodmo_name "sample";
String description "Sample ID number";
String long_name "Sample ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
year {
Int16 _FillValue 32767;
Int16 actual_range 2010, 2014;
String bcodmo_name "year";
String description "Year of sample; YYYY";
String long_name "Year";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "unitless";
}
month {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 4, 11;
String bcodmo_name "month";
String description "Month of sampling; MM";
String long_name "Month";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/MNTHXXXX/";
String units "unitless";
}
day {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 31;
String bcodmo_name "day";
String description "Day of sampling; DD";
String long_name "Day";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DAYXXXXX/";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 25.31, 29.17;
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 -93.6, -84.82;
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 2.0, 3342.42;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Depth at which sample was taken";
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";
}
salinity {
Float32 _FillValue NaN;
Float32 actual_range 32.04, 36.76;
String bcodmo_name "sal";
Float64 colorBarMaximum 37.0;
Float64 colorBarMinimum 32.0;
String description "Salinity of water sample";
String long_name "Sea Water Practical Salinity";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/";
String units "practical salinity units (PSU)";
}
pressure {
Float32 _FillValue NaN;
Float32 actual_range 2.01, 3391.13;
String bcodmo_name "pressure";
String description "Pressure at depth";
String long_name "Pressure";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PRESPR01/";
String units "decibar (dbar)";
}
temperature {
Float32 _FillValue NaN;
Float32 actual_range 4.26, 28.97;
String bcodmo_name "temperature";
String description "Temperature at depth";
String long_name "Temperature";
String units "celsius";
}
measured_temp {
Float32 _FillValue NaN;
Float32 actual_range 2.35, 27.3;
String bcodmo_name "temperature";
String description "Temperature of sample after being standardized in 25 degree celsius water bath for 10-20 minutes.";
String long_name "Measured Temp";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/";
String units "celsius";
}
input_pH {
Float32 _FillValue NaN;
Float32 actual_range 7.58, 8.44;
String bcodmo_name "pH";
String description "pH measurement of sample (total scale)";
String long_name "Input P H";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/";
String units "total pH scale";
}
TA {
Float32 _FillValue NaN;
Float32 actual_range 2201.39, 2410.12;
String bcodmo_name "TALK";
String description "Total alkalinity of sample";
String long_name "TA";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/MDMAP014/";
String units "micromoles per killigram (umol/kg)";
}
nTA {
Float32 _FillValue NaN;
Float32 actual_range 2184.47, 2514.59;
String bcodmo_name "TALK";
String description "Salinity normalized total alkalinity";
String long_name "N TA";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/MDMAP014/";
String units "micromoles per killigram (umol/kg)";
}
pHT {
Float32 _FillValue NaN;
Float32 actual_range 7.79, 8.26;
String bcodmo_name "pH";
String description "pH measured on the total hydrogen scale";
String long_name "P HT";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PHXXZZXX/";
String units "total pH scale";
}
omega_aragonite {
Float32 _FillValue NaN;
Float32 actual_range 0.99, 4.43;
String bcodmo_name "OM_ar";
String description "saturation state of aragonite";
String long_name "Omega Aragonite";
String units "unitless";
}
DIC {
Float32 _FillValue NaN;
Float32 actual_range 1904.27, 2240.77;
String bcodmo_name "DIC";
String description "Dissolved inorganic carbon values";
String long_name "DIC";
String units "micromoles per killigram (umol/kg)";
}
pCO2 {
Float32 _FillValue NaN;
Float32 actual_range 221.94, 720.36;
String bcodmo_name "pCO2";
String description "Carbond dioxide concentration";
String long_name "P CO2";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PCO2C101/";
String units "microatomospheres (uatm)";
}
revelle_factor {
Float32 _FillValue NaN;
Float32 actual_range 8.42, 16.96;
String bcodmo_name "unknown";
String description "A measure inversely proportional to the capacity for seawater to absorb atmospheric CO2";
String long_name "Revelle Factor";
String units "unitless";
}
bicarbonate_ion {
Float32 _FillValue NaN;
Float32 actual_range 1619.96, 2123.24;
String bcodmo_name "bicarbonate";
String description "Bicarbonate ion concentration";
String long_name "Bicarbonate Ion";
String units "micromoles per killigram (umol/kg)";
}
carbonate_ion {
Float32 _FillValue NaN;
Float32 actual_range 77.14, 277.75;
String bcodmo_name "carbonate";
String description "Carbonate ion concentration";
String long_name "Carbonate Ion";
String units "micromoles per killigram (umol/kg)";
}
TA_DIC {
Float32 _FillValue NaN;
Float32 actual_range 1.04, 1.21;
String bcodmo_name "unknown";
String description "Total alkalinity and dissolved inorganic carbon ratio";
String long_name "TA DIC";
String units "unitless";
}
comments {
String bcodmo_name "comment";
String description "Comments";
String long_name "Comments";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"pH was measured on the total hydrogen scale (pHT) within one hour of sample
collection. Each water sample was placed in a 25 degrees C water bath for
10\\u201320 minutes to standardize temperature (mean temperature over all pH
measurements of 22.2 +/- 2.6 degrees C). pHT was then measured in duplicate
using the Orion 5 Star pH meter and glass electrode (ROSS Ultra pH/ATC Triode
8107BNUMD) calibrated with Tris\\u2013HCL buffer solution obtained from the
Dickson Lab (Batch 22). Electrode performance was regularly checked against
standard Tris-HCl and AMP-HCl buffers in artificial seawater (Nemzer et al.
2005; Dickson et al. 2007). Temperature was measured using the integrated
temperature sensor on the ROSS Ultra pH/ATC Triode from 2010\\u20132013, and
using a handheld thermocouple (Omega\\u00a0HH81A) in 2014. Total alkalinity
(TA) was measured in triplicate by acid titration on a Mettler\\u2013Toledo
DL15 autotitrator using 0.1 mol L\\u20131 HCl buffered in 0.6 mol L\\u20131 NaCl
(modified from SOP 3b, Dickson et al. 2007). The autotitrator was calibrated
daily on the NBS scale using certified reference buffers (Orion), and
certified reference materials (Dickson Lab, batches 138 and 141) were measured
periodically to ensure accuracy (within +/- 10 umol kg-1).\\u00a0";
String awards_0_award_nid "54992";
String awards_0_award_number "OCE-1220478";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1220478";
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
"Carbonate Data
E. Cordes & R. Kulathinal, PIs
Version 16 September 2016";
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 "2016-09-16T22:09:36Z";
String date_modified "2019-06-11T19:38:43Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.658946.1";
Float64 Easternmost_Easting -84.82;
Float64 geospatial_lat_max 29.17;
Float64 geospatial_lat_min 25.31;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -84.82;
Float64 geospatial_lon_min -93.6;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 3342.42;
Float64 geospatial_vertical_min 2.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-12-21T17:53:11Z (local files)
2024-12-21T17:53:11Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_658946.html";
String infoUrl "https://www.bco-dmo.org/dataset/658946";
String institution "BCO-DMO";
String instruments_0_acronym "CTD";
String instruments_0_dataset_instrument_description "Water samples taken from CTD casts";
String instruments_0_dataset_instrument_nid "658955";
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 "CTD";
String instruments_1_acronym "Water Temp Sensor";
String instruments_1_dataset_instrument_description "Sensor that measured water temperature";
String instruments_1_dataset_instrument_nid "659584";
String instruments_1_description "General term for an instrument that measures the temperature of the water with which it is in contact (thermometer).";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/134/";
String instruments_1_instrument_name "Water Temperature Sensor";
String instruments_1_instrument_nid "647";
String instruments_1_supplied_name "Temperature sensor";
String instruments_2_acronym "pH Sensor";
String instruments_2_dataset_instrument_description "pHT was measured using this instrument";
String instruments_2_dataset_instrument_nid "659585";
String instruments_2_description "General term for an instrument that measures the pH or how acidic or basic a solution is.";
String instruments_2_instrument_name "pH Sensor";
String instruments_2_instrument_nid "674";
String instruments_2_supplied_name "Orion 5 Star pH themeter";
String instruments_3_acronym "Automatic titrator";
String instruments_3_dataset_instrument_description "Measured total alkalinity";
String instruments_3_dataset_instrument_nid "658957";
String instruments_3_description "Instruments that incrementally add quantified aliquots of a reagent to a sample until the end-point of a chemical reaction is reached.";
String instruments_3_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB12/";
String instruments_3_instrument_name "Automatic titrator";
String instruments_3_instrument_nid "682";
String instruments_3_supplied_name "Mettler-Toledo EL15 autotitrator";
String instruments_4_acronym "Aquarium";
String instruments_4_dataset_instrument_description "Experiments conducted using aquaria";
String instruments_4_dataset_instrument_nid "659586";
String instruments_4_description "Aquarium - a vivarium consisting of at least one transparent side in which water-dwelling plants or animals are kept";
String instruments_4_instrument_name "Aquarium";
String instruments_4_instrument_nid "711";
String instruments_4_supplied_name "Aquarium";
String instruments_5_acronym "Bottle";
String instruments_5_dataset_instrument_description "Water samples collected by vehicle-mounted bottle";
String instruments_5_dataset_instrument_nid "658956";
String instruments_5_description "A container, typically made of glass or plastic and with a narrow neck, used for storing drinks or other liquids.";
String instruments_5_instrument_name "Bottle";
String instruments_5_instrument_nid "542498";
String instruments_5_supplied_name "Vehicle mounted bottle";
String keywords "aragonite, bco, bco-dmo, bicarbonate, bicarbonate_ion, biological, carbon, carbon dioxide, carbonate, carbonate_ion, chemical, co2, co3, comments, cruise, cruise_id, cruise_name, data, dataset, day, density, depth, dic, dioxide, dmo, earth, Earth Science > Oceans > Salinity/Density > Salinity, erddap, factor, input, input_pH, instrument, ion, latitude, longitude, management, measured, measured_temp, measurement, measurement_location, month, name, nTA, ocean, oceanography, oceans, office, omega, omega_aragonite, pCO2, pHT, practical, preliminary, pressure, revelle, revelle_factor, salinity, sample, sample_ID, science, sea, sea_water_practical_salinity, seawater, site, TA_DIC, temperature, water, year";
String keywords_vocabulary "GCMD Science Keywords";
String license "https://www.bco-dmo.org/dataset/658946/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/658946";
Float64 Northernmost_Northing 29.17;
String param_mapping "{'658946': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/658946/parameters";
String people_0_affiliation "Temple University";
String people_0_affiliation_acronym "Temple";
String people_0_person_name "Erik E Cordes";
String people_0_person_nid "51539";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Temple University";
String people_1_affiliation_acronym "Temple";
String people_1_person_name "Dr Robert J. Kulathinal";
String people_1_person_nid "51540";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Temple University";
String people_2_affiliation_acronym "Temple";
String people_2_person_name "Erik E Cordes";
String people_2_person_nid "51539";
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 "Hannah Ake";
String people_3_person_nid "650173";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "Lophelia OA";
String projects_0_acronym "Lophelia OA";
String projects_0_description
"The Gulf of Mexico deep water ecosystems are threatened by the persistent threat of ocean acidification. Deep-water corals will be among the first to feel the effects of this process, in particular the deep-water scleractinians that form their skeleton from aragonite. The continued shoaling of the aragonite saturation horizon (the depth below which aragonite is undersaturated) will place many of the known, and as yet undiscovered, deep-water corals at risk in the very near future. The most common deep-water framework-forming scleractinian in the world's oceans is Lophelia pertusa. This coral is most abundant in the North Atlantic, where aragonite saturation states are relatively high, but it also creates extensive reef structures between 300 and 600 m depth in the Gulf of Mexico where aragonite saturation states were previously unknown. Preliminary data indicate that pH at this depth range is between 7.85 and 8.03, and the aragonite saturation state is typically between 1.28 and 1.69. These are the first measurements of aragonite saturation state for the deep Gulf of Mexico, and are among the lowest Aragonite saturation state yet recorded for framework-forming corals in any body of water, at any depth.
This project will examine the effects of ocean acidification on L. pertusa, combining laboratory experiments, rigorous oceanographic measurements, the latest genome and transcriptome sequencing platforms, and quantitative PCR and enzyme assays to examine changes in coral gene expression and enzyme activity related to differences in carbonate chemistry. Short-term and long-term laboratory experiments will be performed at Aragonite saturation state of 1.45 and 0.75 and the organismal (e.g., survivorship and calcification rate) and genetic (e.g., transcript abundance) responses of the coral will be monitored. Genomic DNA and RNA will be extracted, total mRNA purified, and comprehensive and quantitative profiles of the transcriptome generated using a combination of 454 and Illumina sequencing technologies. Key genes in the calcification pathways as well as other differentially expressed genes will be targeted for specific qPCR assays to verify the Illumina sequencing results. On a research cruise, L. pertusa will be sampled (preserved at depth) along a natural gradient in carbonate chemistry, and included in the Illumina sequencing and qPCR assays. Water samples will be obtained by submersible-deployed niskin bottles adjacent to the coral collections as well as CTD casts of the water column overlying the sites. Water samples will be analyzed for pH, alkalinity, nitrates and soluble reactive phosphorus. These will be used in combination with historical data in a model to hindcast Aragonite saturation state.
This project will provide new physiological and genetic data on an ecologically-significant and anthropogenically-threatened deepwater coral in the Gulf of Mexico. An experimental system, already developed by the PIs, offers controlled conditions to test the effect of Aragonite saturation state on calcification rates in scleractinians and, subsequently, to identify candidate genes and pathways involved in the response to reduced pH and Aragonite saturation state. Both long-term and population sampling experiments will provide additional transcriptomic data and specifically investigate the expression of the candidate genes. These results will contribute to our understanding of the means by which scleractinians may acclimate and acclimatize to low pH, alkalinity, and Aragonite saturation state. Furthermore, the investigators will continue a time series of oceanographic measurements of the carbonate system in the Gulf of Mexico, which will allow the inclusion of this significant body of water in models of past and future ocean acidification scenarios.";
String projects_0_end_date "2015-08";
String projects_0_geolocation "Northern Gulf of Mexico";
String projects_0_name "Physiological and genetic responses of the deep-water coral, Lophelia pertusa, to ongoing ocean acidification in the Gulf of Mexico";
String projects_0_project_nid "2224";
String projects_0_start_date "2012-09";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 25.31;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Water samples from CTD casts and vehicle-mounted bottles from the R/V Atlantis, R/V Ronald Brown, R/V Falkor, & E/V Nautilus in the Gulf of Mexico & Florida from 2010 to 2014 (Lophelia OA project)";
String title "[Carbonate data from water samples] - Water samples from CTD casts and vehicle-mounted bottles from the R/V Atlantis, R/V Ronald Brown, R/V Falkor, & E/V Nautilus in the Gulf of Mexico & Florida from 2010 to 2014 (Lophelia OA project) (Physiological and genetic responses of the deep-water coral, Lophelia pertusa, to ongoing ocean acidification in the Gulf of Mexico)";
String version "1";
Float64 Westernmost_Easting -93.6;
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.