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Dataset Title:  Carbon near edge X-ray absorption fine structure (NEXAFS) spectra from pelagic
sediment from the North Atlantic gyre, South Pacific gyre, and Peru Basin from
cruises KN223 (R/V Knorr), KNOX02RR (R/V Roger Revelle), and ODP leg 201
between 2002 and 2014
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_815380)
Range: longitude = -165.64333 to -50.62°E, latitude = 12.01667 to 45.96333°N, depth = 3705.0 to 5699.0m
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
 
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Things You Can Do With Your Graphs

Well, you can do anything you want with your graphs, of course. But some things you might not have considered are:

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  location {
    String bcodmo_name "site";
    String description "Sample origin";
    String long_name "Location";
    String units "unitless";
  }
  expedition {
    String bcodmo_name "cruise_id";
    String description "Cruise name";
    String long_name "Expedition";
    String units "unitless";
  }
  date {
    String bcodmo_name "date";
    String description "date sample collection in ISO 8601 format 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 12.01667, 45.96333;
    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 -165.64333, -50.62;
    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";
  }
  depth {
    String _CoordinateAxisType "Height";
    String _CoordinateZisPositive "down";
    Float64 _FillValue NaN;
    Float64 actual_range 3705.0, 5699.0;
    String axis "Z";
    String bcodmo_name "depth";
    String description "Water depth";
    String ioos_category "Location";
    String long_name "Water Depth";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
    String positive "down";
    String standard_name "depth";
    String units "m";
  }
  core_type {
    String bcodmo_name "sample_type";
    String description "Coring device used";
    String long_name "Core Type";
    String units "unitless";
  }
  core_depth {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0125, 112.65;
    String bcodmo_name "meters below seafloor";
    String description "Sample depth (meters below seafloor)";
    String long_name "Core Depth";
    String units "meters (m)";
  }
  site {
    String bcodmo_name "site";
    String description "Site number";
    String long_name "Site";
    String units "unitless";
  }
  sample_comment {
    String bcodmo_name "comment";
    String description "Comment about sample";
    String long_name "Sample Comment";
  }
  absorption {
    Float32 _FillValue NaN;
    Float32 actual_range -1.28061, 13.96284;
    String bcodmo_name "absorbance";
    String description "absorption. arbitrary units (normalized)";
    String long_name "Absorption";
    String units "unitless";
  }
  eV {
    Float64 _FillValue NaN;
    Float64 actual_range 280.0, 320.0;
    String bcodmo_name "eV";
    String description "electron volts (incident energy)";
    String long_name "E V";
    String units "electron volts (eV)";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
    String acquisition_description 
"See Estes el al. (2019) for complete methods.
 
Sediment slurries were generated by subsampling ~0.1 g of wet sediment from
samples stored at 4 \\u00b0C into a sterile microcentrifuge tube. Then,
0.2\\u20130.5 ml of 0.2 \\u03bcm filtered 18 M\\u03a9 water was added  
 and the sample shaken. Sediment slurry (1\\u201310 \\u03bcl) was pipetted onto
silicon wafers and air-dried. The beamline was operated with a 500 l mm\\u20131
spherical grating monochromator and entrance and exit slits set to 40 \\u03bcm,
which yielded an absolute energy resolution of less than 0.3 eV. The samples
were attached to an aluminium sample stick in a single load and analysed under
ultrahigh vacuum conditions (pressure ~10\\u22129 mbar). The measurements were
made in the total electron yield (TEY) mode on a spot size of less than 1 mm2
using a grazing incidence angle  
 of 45\\u00b0, where previous trials determined that the incidence angle did
not yield a  
 difference in results. The TEY mode was selected instead of fluorescence as
we observed dampening of the fluorescence signal, probably due to matrix-
induced absorption.
 
Spectra were collected around the C 1s edge, from 260 to 340 eV, with a dwell
time of 0.2 s. To avoid beam damage and variation of the background due to
charging, scans were taken at different positions on the sample. The spectra
analysed were the average of 2\\u20133 scans taken at different positions on
the sample. The dark current was measured prior to the collection of each
spectrum and subtracted from the raw data. Spectra were then normalized to no
load current measured by a mesh upstream of the chamber with freshly
evaporated gold.
 
Instruments:
 
Bulk carbon NEXAFS spectroscopy was conducted on beamlines 8-2 and 10-1 at the
Stanford Synchrotron Radiation Lightsource.
 
The absolute energy calibration of the carbon spectra was achieved by shifting
the energy such that the first dip in the incoming intensity due to carbon
contamination on the beamline optics (carbon dip) occurred at 284.7 eV.";
    String awards_0_award_nid "554980";
    String awards_0_award_number "OCE-0939564";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0939564";
    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 
"Carbon NEXAFS bulk data 
  PI: Emily Estes 
  Data Version 1: 2020-07-22";
    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 dataset_current_state "Final and no updates";
    String date_created "2020-06-15T21:58:56Z";
    String date_modified "2020-07-23T15:27:52Z";
    String defaultDataQuery "&time<now";
    String doi "10.26008/1912/bco-dmo.815380.1";
    Float64 Easternmost_Easting -50.62;
    Float64 geospatial_lat_max 45.96333;
    Float64 geospatial_lat_min 12.01667;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -50.62;
    Float64 geospatial_lon_min -165.64333;
    String geospatial_lon_units "degrees_east";
    Float64 geospatial_vertical_max 5699.0;
    Float64 geospatial_vertical_min 3705.0;
    String geospatial_vertical_positive "down";
    String geospatial_vertical_units "m";
    String history 
"2021-10-15T20:28:10Z (local files)
2021-10-15T20:28:10Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_815380.das";
    String infoUrl "https://www.bco-dmo.org/dataset/815380";
    String institution "BCO-DMO";
    String instruments_0_acronym "Spectrometer";
    String instruments_0_dataset_instrument_description "Bulk carbon synchrotron-based near edge x-ray fine structure (NEXAFS) spectroscopy was conducted on beamlines 8-2 and 10-1 at the Stanford Synchrotron Radiation Lightsource.";
    String instruments_0_dataset_instrument_nid "815390";
    String instruments_0_description "A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/";
    String instruments_0_instrument_name "Spectrometer";
    String instruments_0_instrument_nid "667";
    String keywords "absorption, bco, bco-dmo, biological, chemical, comment, core, core_depth, core_type, data, dataset, date, depth, dmo, erddap, expedition, latitude, longitude, management, oceanography, office, preliminary, sample, sample_comment, site, time, type, v, water, water_depth";
    String license "https://www.bco-dmo.org/dataset/815380/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/815380";
    Float64 Northernmost_Northing 45.96333;
    String param_mapping "{'815380': {'latitude': 'master - latitude', 'water_depth': 'master - depth', 'longitude': 'master - longitude'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/815380/parameters";
    String people_0_affiliation "Texas A&M University";
    String people_0_affiliation_acronym "TAMU";
    String people_0_person_name "Emily Estes";
    String people_0_person_nid "779219";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Woods Hole Oceanographic Institution";
    String people_1_affiliation_acronym "WHOI";
    String people_1_person_name "Colleen Hansel";
    String people_1_person_nid "756932";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "Woods Hole Oceanographic Institution";
    String people_2_affiliation_acronym "WHOI BCO-DMO";
    String people_2_person_name "Amber D. York";
    String people_2_person_nid "643627";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "Org C Sed II,Org C Sed I";
    String projects_0_acronym "Org C Sed II";
    String projects_0_description 
"Abstract from the C-DEBI project page:
Sediment underlying ocean gyres receives minimal input of fresh organic matter yet sustains a small but active heterotrophic microbial community. The concentration and composition of the organic carbon (OC) available to this deep biosphere however is unknown. We analyzed the content and composition of OC in pelagic sediment in order to identify mechanism(s) that dictate the balance between OC preservation and utilization by microorganisms. Sediment cores from the North Atlantic gyre (KN223), South Pacific Gyre (Knox02-RR), and Peru Basin (IODP site 1231) allowed for a global comparison and a test of how sediment lithology and redox state affect OC preservation. OC was present in low concentrations in all samples (0.01—0.61%), at depths up to 112 meters below seafloor and estimated sediment ages of up to 50 million years. Synchrotron-based near edge X-ray absorption fine structure (NEXAFS) spectroscopy was conducted on over 100 samples, one of the first applications of NEXAFS to sedimentary environments. NEXAFS revealed an OC reservoir dominated by amide and carboxylic functionalities in a scaffolding of O-alkyl and aliphatic carbons. Detection of extractable, extracellular proteins supports this composition and suggests that sedimentary OC is protein-derived. This composition was common across all sites and depths, implicating physical rather than chemical mechanisms in OC preservation on long timescales. This study thereby points to physical access rather than energy or metabolic potential as a key constraint on subsurface heterotrophic life.";
    String projects_0_end_date "2017-07";
    String projects_0_geolocation "North Atlantic gyre, South Pacific gyre";
    String projects_0_name "Geochemical controls on organic carbon quantity and quality in the deep subsurface";
    String projects_0_project_nid "779216";
    String projects_0_project_website "https://www.darkenergybiosphere.org/award/3d-spatial-mapping-of-the-energetic-return-of-1000-metabolisms-within-the-compositional-variation-of-oceanic-crusts-near-mid-ocean-ridges/";
    String projects_0_start_date "2016-06";
    String projects_1_acronym "Org C Sed I";
    String projects_1_description 
"Abstract from the C-DEBI project page:
Minerals have recently been identified as a primary host for organic carbon (OC) within marine sediments. This strong physical and chemical carbon-mineral association is believed to reduce, and in some cases completely eliminate, the bioavailablilty of this carbon for microbial life. The paucity of information regarding the nature of this carbon-mineral association and the composition of the hosted carbon, however, precludes our ability to predict the ultimate fate of this OC and its involvement in deep subsurface life. Here, we addressed this knowledge gap by using a suite of bulk and spatially-resolved geochemical and mineralogical techniques to characterize OC-mineral associations within the deep subsurface. We characterized sediment samples collected on the 2014 North Atlantic long coring expedition (KN223) in the western subtropical North Atlantic that included three geochemically distinct long cores to a depth of 24-30 m and spanned OC-limited oxic to anoxic sediments. We find measurable and relevant OC concentrations throughout the sediment cores, that decreases linearly over ~25 meters burial depth, from ~0.15 to 0.075 mol OC/kg solid. OC within the sediments is compositionally complex on both a macro- and micro-scale, spanning a gradient of lability even at depth. Proteins are observed throughout the sediment depth profiles, where they appear to constitute a substantial fraction of the TOC. Correspondingly, a low C:N ratio is observed, consistent with proteinaceous carbon within the sediments. In sum, these findings point to a substantial mineral-hosted OC reservoir within the deep subsurface that may fuel the deep biosphere and select for protein-based heterotrophy.";
    String projects_1_end_date "2016-03";
    String projects_1_geolocation "North Atlantic gyre, South Pacific gyre";
    String projects_1_name "Elucidating the extent and composition of mineral-hosted carbon in the deep biosphere";
    String projects_1_project_nid "779223";
    String projects_1_project_website "https://www.darkenergybiosphere.org/award/elucidating-the-extent-and-composition-of-mineral-hosted-carbon-in-the-deep-biosphere/";
    String projects_1_start_date "2015-04";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 12.01667;
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "Carbon near edge X-ray absorption fine structure (NEXAFS) spectra from pelagic sediment from the North Atlantic gyre, South Pacific gyre, and Peru Basin from cruises KN223 (R/V Knorr), KNOX02RR (R/V Roger Revelle), and ODP leg 201 between 2002 and 2014.";
    String title "Carbon near edge X-ray absorption fine structure (NEXAFS) spectra from pelagic sediment from the North Atlantic gyre, South Pacific gyre, and Peru Basin from cruises KN223 (R/V Knorr), KNOX02RR (R/V Roger Revelle), and ODP leg 201 between 2002 and 2014";
    String version "1";
    Float64 Westernmost_Easting -165.64333;
    String xml_source "osprey2erddap.update_xml() v1.5";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

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.


 
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