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Dataset Title:  HPLC pigment analyses of CTD-collected samples from R/V Knorr cruise KN207-03
in the North Atlantic (transect from Ponta Delgada, Azores to Reykjavik,
Iceland) in 2012 (NA-VICE project)
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_517634)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Files | Make a graph
 
Variable ?   Optional
Constraint #1 ?
Optional
Constraint #2 ?
   Minimum ?
 
   Maximum ?
 
 cast (alphanumeric) ?          "101*"    "CTD_097"
 station (text) ?          "Bullseye"    "cyclops_eye"
 date_gmt (unitless) ?          "06172012"    "NaN"
 time_gmt (unitless) ?          "003000"    "NaN"
 date_local (unitless) ?          "06172012"    "NaN"
 time_local (unitless) ?          "003000"    "NaN"
 latitude (degrees_north) ?          42.963    65.447967
  < slider >
 longitude (degrees_east) ?          -35.0733    -26.102033
  < slider >
 lat_deg (Latitude, degrees North) ?          42    65
 lat_min (Latitude, minutes North) ?          0.0    59.83
 lon_deg (Longitude, degrees West) ?          26    35
 lon_min (Longitude, minutes West) ?          0.0    56.884
 time (ISO Date Time UTC, UTC) ?          2012-06-17T11:00:00Z    
  < slider >
 depth (m) ?          3.0    150.0
  < slider >
 amb_bot (integer) ?          "1"    "NaN"
 niskin_sampled (integer) ?          1    24
 niskins_fired (range of integers) ?          "13_thru_16"    "NaN"
 filt_vol (liters (L)) ?          0.96    2.15
 pigment (text) ?          "allox"    "zeax"
 concentration (nanograms per liter (ng/L)) ?          0    2204
 
Server-side Functions ?
 distinct() ?
? ("Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.")

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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  cast {
    String bcodmo_name "cast";
    String description "Cast number.";
    String long_name "Cast";
    String units "alphanumeric";
  }
  station {
    String bcodmo_name "station";
    String description "Station name.";
    String long_name "Station";
    String units "text";
  }
  date_gmt {
    String bcodmo_name "date_gmt";
    String description "Date of cast (GMT). in the format mmddyyyy";
    String long_name "Date Gmt";
    String units "unitless";
  }
  time_gmt {
    String bcodmo_name "time_gmt";
    String description "Time of cast (GMT). in the format hhmmss";
    String long_name "Time Gmt";
    String units "unitless";
  }
  date_local {
    String bcodmo_name "date_local";
    String description "Date of cast (local time zone). in the format mmddyyyy";
    String long_name "Date Local";
    String units "unitless";
  }
  time_local {
    String bcodmo_name "time_local";
    String description "Time of cast (local time zone). in the format hhmmss";
    String long_name "Time Local";
    String units "unitless";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float64 _FillValue NaN;
    Float64 actual_range 42.963, 65.447967;
    String axis "Y";
    String bcodmo_name "latitude";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "Latitude. Positive values = North.";
    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 -35.0733, -26.102033;
    String axis "X";
    String bcodmo_name "longitude";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "Longitude. Positive values = East.";
    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";
  }
  lat_deg {
    Byte _FillValue 127;
    Byte actual_range 42, 65;
    String bcodmo_name "lat_degs";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "Degrees latitude.";
    String long_name "Latitude";
    String standard_name "latitude";
    String units "degrees North";
  }
  lat_min {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 59.83;
    String bcodmo_name "lat_mins";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "Minutes latitude.";
    String long_name "Latitude";
    String standard_name "latitude";
    String units "minutes North";
  }
  lon_deg {
    Byte _FillValue 127;
    Byte actual_range 26, 35;
    String bcodmo_name "lon_degs";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "Degrees longitude. Positive = West.";
    String long_name "Longitude";
    String standard_name "longitude";
    String units "degrees West";
  }
  lon_min {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 56.884;
    String bcodmo_name "lon_mins";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "Minutes longitude. Positive = West.";
    String long_name "Longitude";
    String standard_name "longitude";
    String units "minutes West";
  }
  time {
    String _CoordinateAxisType "Time";
    Float64 actual_range 1.3399308e+9, NaN;
    String axis "T";
    String bcodmo_name "ISO_DateTime_UTC";
    String description "Date and time of cast formatted to ISO8601 standard.";
    String ioos_category "Time";
    String long_name "ISO Date Time UTC";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/";
    String standard_name "time";
    String time_origin "01-JAN-1970 00:00:00";
    String units "seconds since 1970-01-01T00:00:00Z";
  }
  depth {
    String _CoordinateAxisType "Height";
    String _CoordinateZisPositive "down";
    Float64 _FillValue NaN;
    Float64 actual_range 3.0, 150.0;
    String axis "Z";
    String bcodmo_name "depth";
    Float64 colorBarMaximum 8000.0;
    Float64 colorBarMinimum -8000.0;
    String colorBarPalette "TopographyDepth";
    String description "Depth of Niskin bottle firing.";
    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";
  }
  amb_bot {
    String bcodmo_name "bottle";
    String description "Amber bottle identification number.";
    String long_name "Amb Bot";
    String units "integer";
  }
  niskin_sampled {
    Byte _FillValue 127;
    Byte actual_range 1, 24;
    String bcodmo_name "bottle";
    String description "Niskin bottle number from which HPLC sample was taken.";
    String long_name "Niskin Sampled";
    String units "integer";
  }
  niskins_fired {
    String bcodmo_name "bots";
    String description "Niskin bottle numbers fired at depth; HPLC sample was taken from one Niskin bottle.";
    String long_name "Niskins Fired";
    String units "range of integers";
  }
  filt_vol {
    Float32 _FillValue NaN;
    Float32 actual_range 0.96, 2.15;
    String bcodmo_name "fluor_vol_filt";
    String description "Volume of water filtered.";
    String long_name "Filt Vol";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/VOLFMCXX/";
    String units "liters (L)";
  }
  pigment {
    String bcodmo_name "pigment_concentration";
    String description 
"Name of the pigment measured:
chl_c3 = Chlorophyll c3;
chl_ide = Chlorophyllide a;
mg_dvp = Magnesium-2;4-divinyl phaeoporphyrin a5 monomethyl ester;
chl_c2 = Chlorophyll c2;
chl_c1 = Chlorophyll c1;
peridinin = Peridinin;
but19 = 19-butanoyloxyfucoxanthin;
fucox = Fucoxanthin;
ph_ide = Pheophorbide a;
neox = Neoxanthin;
prasinox = Prasinoxanthin;
violax = Violaxanthin;
hex19 = 19'-hexanoyloxyfucoxanthin;
diadinox = Diadinoxanthin;
cis_fucox = cis-Fucoxanthin;
allox = Alloxanthin;
diatox = Diatoxanthin;
monad = Monadoxanthin;
zeax = Zeaxanthin;
lutein = lutein;
crocox = Crocoxanthin;
chl_b = Chlorophyll b;
dv_chl_a = Divinyl Chlorophyll a;
chl_a = Chlorophyll a;
p_phytin = Phaeophytin a;
carotene_a = alpha Carotene;
carotene_b = beta Carotene.";
    String long_name "Pigment";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/OPWC/";
    String units "text";
  }
  concentration {
    Int16 _FillValue 32767;
    Int16 actual_range 0, 2204;
    String bcodmo_name "pigment_concentration";
    String description "Concentration of the pigment as determined by HPLC.";
    String long_name "Concentration";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/OPWC/";
    String units "nanograms per liter (ng/L)";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
    String acquisition_description 
"Water samples were collected from CTD Niskin bottles. Water samples for HPLC
analyses were taken from one Niskin bottle per cast-depth combination included
in the dataset. Note that the niskin_sampled column indicates which Niskin
bottle the HPLC sample was taken from. The niskins_fired column indicates all
Niskin bottle numbers fired at the specified depth, though the HPLC sample was
taken from only one of those bottles.
 
Chlorophyll and accessory pigment composition was analyzed by high performance
liquid chromatography (HPLC; Agilent 1100). Culture aliquots were filtered on
Whatmann GF/F filters, flash frozen in liquid nitrogen, and stored at
-80\\u00b0C until analysis. Just prior to analysis, pigments were extracted
overnight in acetone at -20\\u00b0C. The following day extracted pigments were
centrifuged and measured using a gradient elution method (DiTullio and Geesey,
2003), a modification of the Zapata et al 2000 method. Chromatographic
separation was performed using a Waters C8 symmetry column, photodiode array
and fluorescence detectors. The internal standard, \\u03b2-Apo-8-carotenal-
trans standard (Fluka Chemical Corp., USA) was added to extracted pigments as
a peak reference. Individual pigment peaks were quantified with Chemstation
software (revision B.03.01, Agilent) and our pigment action spectra library
calibrated using pigment standards from DHI LABS (Hoersholm, Denmark) and in-
house purifications of non-commercially available pigments. Coefficient of
variation among replicate HPLC injections is < 3% and our limit of detection
is approximately 1 ng L-1.";
    String awards_0_award_nid "54870";
    String awards_0_award_number "OCE-1061876";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1061876";
    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 
"HPLC Pigments 
  PI: Giacomo R. DiTullio 
  Contact: Emily Cooper 
  Version History: 
   Current version:  17 Sept 2014 
   Dataset revised:  12 Sept 2014 
   Original dataset: 26 June 2014";
    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 "2014-06-26T15:57:25Z";
    String date_modified "2019-12-30T15:40:59Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.1575/1912/bco-dmo.517634.1";
    Float64 Easternmost_Easting -26.102033;
    Float64 geospatial_lat_max 65.447967;
    Float64 geospatial_lat_min 42.963;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -26.102033;
    Float64 geospatial_lon_min -35.0733;
    String geospatial_lon_units "degrees_east";
    Float64 geospatial_vertical_max 150.0;
    Float64 geospatial_vertical_min 3.0;
    String geospatial_vertical_positive "down";
    String geospatial_vertical_units "m";
    String history 
"2022-08-10T23:23:23Z (local files)
2022-08-10T23:23:23Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_517634.html";
    String infoUrl "https://www.bco-dmo.org/dataset/517634";
    String institution "BCO-DMO";
    String instruments_0_acronym "Niskin bottle";
    String instruments_0_dataset_instrument_nid "517688";
    String instruments_0_description "A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends.  The bottles can be attached individually on a hydrowire or deployed in 12, 24 or 36 bottle Rosette systems mounted on a frame and combined with a CTD.  Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/";
    String instruments_0_instrument_name "Niskin bottle";
    String instruments_0_instrument_nid "413";
    String instruments_0_supplied_name "Niskin bottle";
    String instruments_1_acronym "HPLC";
    String instruments_1_dataset_instrument_description "Chlorophyll and accessory pigment composition was analyzed by high performance liquid chromatography (HPLC; Agilent 1100).";
    String instruments_1_dataset_instrument_nid "517637";
    String instruments_1_description "A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase.";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB11/";
    String instruments_1_instrument_name "High Performance Liquid Chromatograph";
    String instruments_1_instrument_nid "506";
    String instruments_1_supplied_name "HPLC";
    String keywords "amb, amb_bot, bco, bco-dmo, biological, bot, cast, chemical, concentration, data, dataset, date, date_gmt, date_local, depth, dmo, erddap, filt, filt_vol, fired, iso, ISO_DateTime_UTC, lat_deg, lat_min, latitude, local, lon_deg, lon_min, longitude, management, niskin, niskin_sampled, niskins, niskins_fired, oceanography, office, pigment, preliminary, sampled, station, time, time_gmt, time_local, vol";
    String license "https://www.bco-dmo.org/dataset/517634/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/517634";
    Float64 Northernmost_Northing 65.447967;
    String param_mapping "{'517634': {'lat': 'flag - latitude', 'depth': 'flag - depth', 'lon': 'flag - longitude', 'ISO_DateTime_UTC': 'flag - time'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/517634/parameters";
    String people_0_affiliation "Grice Marine Laboratory - College of Charleston";
    String people_0_affiliation_acronym "GML-CoC";
    String people_0_person_name "Giacomo DiTullio";
    String people_0_person_nid "50689";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Grice Marine Laboratory - College of Charleston";
    String people_1_affiliation_acronym "GML-CoC";
    String people_1_person_name "Emily Cooper";
    String people_1_person_nid "517640";
    String people_1_role "Contact";
    String people_1_role_type "related";
    String people_2_affiliation "Woods Hole Oceanographic Institution";
    String people_2_affiliation_acronym "WHOI BCO-DMO";
    String people_2_person_name "Shannon Rauch";
    String people_2_person_nid "51498";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "NA-VICE";
    String projects_0_acronym "NA-VICE";
    String projects_0_description 
"This project is also called \"NA-VICE\" (North Atlantic Virus Infection of Coccolithophores Expedition).
Project description from NSF award abstract:
Despite the critical importance of viruses in shaping marine microbial ecosystems, very little is known about the molecular mechanisms mediating phytoplankton-virus interactions. As a consequence, we currently lack biomarkers to quantify active viral infection in the oceans, significantly hindering our understanding of its ecological and biogeochemical impacts.
The coccolithophore Emiliania huxleyi (Prymnesiophyceae, Haptophyte) is a cosmopolitan unicellular photoautotroph whose calcite skeletons account for about a third of the total marine CaCO3 production. E. huxleyi forms massive annual spring blooms in the North Atlantic that are infected and terminated by lytic, giant double-stranded DNA containing coccolithoviruses. Findings that lytic viral infection of E. huxleyi recruits the hosts programmed cell death (PCD) machinery demonstrate that viruses employ a sophisticated, co-evolutionary “arms race” in mediating host-virus interactions. The investigators recently demonstrated that viral glycosphingolipids (vGSLs), derived from unexpected cluster of sphingolipid biosynthetic genes, a pathway never before described in a viral genome, play a crucial functional role in facilitating infection of E. huxleyi. The observations of vGSLs in the North Atlantic and Norwegian fjords further suggest that they may be novel, diagnostic biomarkers for viral infection of coccolithophore populations. At the same time, the discovery of vGSLs and a distinct, protective 802 lipid argues that a host-virus, co-evolutionary chemical arms race plays a pivotal role in regulating viral infection and in lubricating upper ocean biogeochemical fluxes of carbon and sulfur.
The focus of this collaborative research project is to elucidate the molecular, ecological, and biogeochemical links between vGSLs (and other polar lipids) and the global cycles of carbon and sulfur.
The team of investigators proposes a multi-pronged approach combing a suite of lab-based, mechanistic studies using several haptophyte-virus model systems along with observational studies and manipulative field-based experiments the Northeast Atlantic. Using these diagnostic markers, they will document active viral infection of natural coccolithophore populations and couple it with a suite of oceanographic measurements in order to quantify how viral infection (via vGSLs) influences cell fate, the dissolved organic carbon (DOC) pool, vertical export of particular organic (POC) and inorganic carbon (PIC; as calcium carbonate, CaCO3) (along with associated alkenone lipid biomarkers and genetic signatures of viruses and their hosts) and the upper ocean sulfur cycle (via the cycling of dimethylsulfide [DMS] and other biogenic sulfur compounds). Furthermore, given they are unique to viruses, the investigators propose that vGSLs can be used to trace the flow of virally-derived carbon and provide quantitative insights into a “viral shunt” that diverts fixed carbon from higher trophic levels and the deep sea.
The overarching hypothesis for this study is that vGSLs are cornerstone molecules in the upper ocean, which facilitate viral infection on massive scales and thereby mechanistically \"lubricate\" the biogeochemical fluxes of C and S in the ocean.";
    String projects_0_end_date "2014-02";
    String projects_0_geolocation "North Atlantic; Azores to Iceland";
    String projects_0_name "Lipid lubrication of oceanic carbon and sulfur biogeochemistry via a host-virus chemical arms race";
    String projects_0_project_nid "2136";
    String projects_0_start_date "2011-03";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 42.963;
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "Dataset includes HPLC pigment analyses of CTD collected samples from the KN207-03 cruise (Northeast Atlantic Ocean transect from Azores to Iceland).";
    String time_coverage_start "2012-06-17T11:00:00Z";
    String title "HPLC pigment analyses of CTD-collected samples from R/V Knorr cruise KN207-03 in the North Atlantic (transect from Ponta Delgada, Azores to Reykjavik, Iceland) in 2012 (NA-VICE project)";
    String version "1";
    Float64 Westernmost_Easting -35.0733;
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

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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