Accessing BCO-DMO data
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| Dataset Title: | [Carbon NEXAFS standards] - Carbon near edge X-ray absorption fine structure (NEXAFS) spectra of standard compounds (Geochemical controls on organic carbon quantity and quality in the deep subsurface) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_815362) |
| Information: | Summary
| License
| ISO 19115
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Attributes {
s {
eV {
Float64 _FillValue NaN;
Float64 actual_range 280.0, 320.0;
String bcodmo_name "eV";
String description "incident energy";
String long_name "E V";
String units "electron volts (eV)";
}
BSA {
Float64 _FillValue NaN;
Float64 actual_range -0.00797300853694, 0.45672515810322;
String bcodmo_name "absorbance";
String description "absorption values for protein (bovine serum albumin (BSA)). arbitrary units (normalized)";
String long_name "BSA";
String units "unitless";
}
phenylalanin {
Float64 _FillValue NaN;
Float64 actual_range -0.00189616148905, 0.63686872685069;
String bcodmo_name "absorbance";
String description "absorption values of phenylalanin. arbitrary units (normalized)";
String long_name "Phenylalanin";
String units "unitless";
}
leucine {
Float64 _FillValue NaN;
Float64 actual_range -0.00150841788173, 1.79254321817363;
String bcodmo_name "absorbance";
String description "absorption values of leucine. arbitrary units (normalized)";
String long_name "Leucine";
String units "unitless";
}
agarose {
Float64 _FillValue NaN;
Float64 actual_range -0.00489097551973, 0.46939224944519;
String bcodmo_name "absorbance";
String description "absorption values of agarose. arbitrary units (normalized)";
String long_name "Agarose";
String units "unitless";
}
alginate {
Float64 _FillValue NaN;
Float64 actual_range -0.00417239166851, 0.90592744921794;
String bcodmo_name "absorbance";
String description "absorption values of alginate. arbitrary units (normalized)";
String long_name "Alginate";
String units "unitless";
}
lipo {
Float64 _FillValue NaN;
Float64 actual_range -0.00163233708639, 0.56126001867199;
String bcodmo_name "absorbance";
String description "absorption values of lipo. arbitrary units (normalized)";
String long_name "Lipo";
String units "unitless";
}
phospholipid {
Float64 _FillValue NaN;
Float64 actual_range -7.6736447302e-4, 1.78986871519392;
String bcodmo_name "absorbance";
String description "absorption values of phospholipid. arbitrary units (normalized)";
String long_name "Phospholipid";
String units "unitless";
}
HMWDOM {
Float64 _FillValue NaN;
Float64 actual_range -0.00565777265214, 1.76599418481696;
String bcodmo_name "absorbance";
String description "absorption values of high molecular weight dissolved organic matter (HMWDOM). arbitrary units (normalized)";
String long_name "HMWDOM";
String units "unitless";
}
humic_acid {
Float64 _FillValue NaN;
Float64 actual_range -0.00271618200714, 1.63426099814073;
String bcodmo_name "absorbance";
String description "absorption values of humic acid. arbitrary units (normalized)";
String long_name "Humic Acid";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"See Estes el al. (2019) for complete methods.
1\\u201310 \\u03bcL of standard compounds 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 standards
PI: Emily Estes
Data Version 1: 2020-06-15";
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 "2020-06-15T21:07:20Z";
String date_modified "2020-07-23T15:20:37Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.815362.1";
String history
"2024-11-08T06:05:43Z (local files)
2024-11-08T06:05:43Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_815362.html";
String infoUrl "https://www.bco-dmo.org/dataset/815362";
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 "815379";
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 "acid, agarose, alginate, bco, bco-dmo, biological, bsa, chemical, data, dataset, dmo, erddap, hmwdom, humic, humic_acid, leucine, lipo, management, oceanography, office, phenylalanin, phospholipid, preliminary, v";
String license "https://www.bco-dmo.org/dataset/815362/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/815362";
String param_mapping "{'815362': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/815362/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)";
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Carbon near edge X-ray absorption fine structure (NEXAFS) spectra of standard compounds. These data contain incident energy and absorption values at that energy for a standard compounds.";
String title "[Carbon NEXAFS standards] - Carbon near edge X-ray absorption fine structure (NEXAFS) spectra of standard compounds (Geochemical controls on organic carbon quantity and quality in the deep subsurface)";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.5";
}
}
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.