BCO-DMO ERDDAP
Accessing BCO-DMO data
log in    
Brought to you by BCO-DMO    

ERDDAP > tabledap > Data Access Form ?

Dataset Title:  Measurements of fluorescence of photosystem II in Plocamium cartilagineum
under various and pCO2 and temperature conditions
Subscribe RSS
Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_733238)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Files | Make a graph
 
Variable ?   Optional
Constraint #1 ?
Optional
Constraint #2 ?
   Minimum ?
 
   Maximum ?
 
 Trial (unitless) ?          2    8
 Tank_ID (unitless) ?          0    9
 pCO2 (atm) ?          344    1053
 Temp (degrees Celsius (°C)) ?          15    20
 Plant_ID (unitless) ?          1.1    15.2
 ID (unitless) ?          "t2_1_1.12_w4"    "t8_9_9.5_w2"
 Week (unitless) ?          0    4
 date (unitless) ?          "2014-06-19"    "2015-02-23"
 light (micromole photons/meter^2/second ( µmole photons . m^-2 . s^-1)) ?          0    427
 F (unitless) ?          0.0    334.0
 Fm (unitless) ?          0.0    454.0
 Yield (unitless) ?          0.0    1.0
 rETR (unitless) ?          0.0    1008.5
 qP (unitless) ?          0.0    4.0
 qN (unitless) ?          0.0    11.0
 NPQ (unitless) ?          0.0    28.797
 
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.")

File type: (more info)

(Documentation / Bypass this form ? )
 
(Please be patient. It may take a while to get the data.)


 

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Trial {
    Byte _FillValue 127;
    Byte actual_range 2, 8;
    String bcodmo_name "replicate";
    String description "Trial number of the experiment";
    String long_name "Trial";
    String units "unitless";
  }
  Tank_ID {
    Byte _FillValue 127;
    Byte actual_range 0, 9;
    String bcodmo_name "sample";
    String description "Identifying number of culture pot";
    String long_name "Tank ID";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  }
  pCO2 {
    Int16 _FillValue 32767;
    Int16 actual_range 344, 1053;
    String bcodmo_name "pCO2";
    String description "Partial pressure of CO2 in solution in culture pot";
    String long_name "P CO2";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PCO2C101/";
    String units "atm";
  }
  Temp {
    Byte _FillValue 127;
    Byte actual_range 15, 20;
    String bcodmo_name "temperature";
    String description "Temperature of seawater in culture pot";
    String long_name "Temperature";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/";
    String units "degrees Celsius (°C)";
  }
  Plant_ID {
    Float32 _FillValue NaN;
    Float32 actual_range 1.1, 15.2;
    String bcodmo_name "sample";
    String description "Plant ID number in culture pot";
    String long_name "Plant ID";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  }
  ID {
    String bcodmo_name "sample";
    String description "Unique identifier for every sample; concatenation of trial_tank ID_plant ID_week";
    String long_name "ID";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  }
  Week {
    Byte _FillValue 127;
    Byte actual_range 0, 4;
    String bcodmo_name "time_point";
    String description "Week number of given trial";
    String long_name "Week";
    String units "unitless";
  }
  date {
    String bcodmo_name "date_local";
    String description "date of data collection formatted as yyyy-mm-dd";
    String long_name "Date";
    String source_name "date";
    String time_precision "1970-01-01";
    String units "unitless";
  }
  light {
    Int16 _FillValue 32767;
    Int16 actual_range 0, 427;
    String bcodmo_name "PAR";
    String description "Photosynthetically active radiation (PAR)";
    String long_name "Light";
    String units "micromole photons/meter^2/second ( µmole photons . m^-2 . s^-1)";
  }
  F {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 334.0;
    String bcodmo_name "fluorescence";
    String description "Relative fluorescence of photosystem II";
    String long_name "F";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLPM01/";
    String units "unitless";
  }
  Fm {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 454.0;
    String bcodmo_name "fluorescence";
    String description "Maximum fluorescence";
    String long_name "FM";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLPM01/";
    String units "unitless";
  }
  Yield {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 1.0;
    String bcodmo_name "Fv2Fm";
    String description "Effective (or Optimal if dark-adapted) quantum yield. Calculated as Yield = (Fm - F)/Fm";
    String long_name "Yield";
    String units "unitless";
  }
  rETR {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 1008.5;
    String bcodmo_name "unknown";
    String description "Relative Electron Transport Rate";
    String long_name "R ETR";
    String units "unitless";
  }
  qP {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 4.0;
    String bcodmo_name "unknown";
    String description "Photochemical quenching";
    String long_name "Q P";
    String units "unitless";
  }
  qN {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 11.0;
    String bcodmo_name "unknown";
    String description "Non-photochemical quenching expressed as a fraction of difference between Fm and minimum F";
    String long_name "Q N";
    String units "unitless";
  }
  NPQ {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 28.797;
    String bcodmo_name "unknown";
    String description "Non-photochemical quenching normalized to Fm measured in the light";
    String long_name "NPQ";
    String units "unitless";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Plocamium cartilagineum was collected from Catalina Island in June - Nov. 2014
and Jan. 2015.
 
Culture pots were placed in large thermally insulated coolers in a
temperature-controlled water bath at either 15 or 20\\u00b0C under saturating
illumination of ~150 \\u00b5moles photons/m^2/s. pCO2 treatments were supplied
to closed culture pots by use of a gas mixing system combining Nitrogen,
Oxygen and Carbon Dioxide to specific CO2 partial pressures, 20.9% oxygen and
the balance being Nitrogen.
 
Measurements of\\u00a0chlorophyll fluorescence of photosystem II were made
using a pulse amplitude modulated (PAM) fluorometer in situ in culture pots.
All samples were dark-adapted prior to measurement by placing a leaf clip in
the closed position over the area to be sampled for 5 minutes prior to
measurement. For fluorescence measurements, the fiber optic probe was placed
directly on the leaf clip perpendicular to the sample. The leaf clip was then
opened and a rapid light curve program function was initiated to measure
fluorescence at each of 9 photon flux densities (PFD\\u2019s). PFD\\u2019s of
the light curve generated by the fluorometer were calibrated using an external
LiCor light meter. Following measurement, the leaf clip was removed and the
sample remained in the culture chamber.\\u00a0
 
Data were downloaded from the Diving PAM using WinControl version 3 software
for Diving PAM.
 
Note: Trial 1 was a pilot test of culture system and methodological procedures
so was not used for data collection in the testing of hypotheses.
 
See Supplemental Files for a table of culture conditions for each of the 8
trials (pdf).";
    String awards_0_award_nid "55177";
    String awards_0_award_number "OCE-1316198";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1316198";
    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 
"Rapid Light Curves - PAM 
   Measurements of fluorescence of photosystem II in Plocamium cartilagineum under various and pCO2 and temperature conditions 
      with pulse amplitude modulated (PAM) fluorometer 
   PI: S. Dudgeon, J. Kubler (CSUN) 
   version: 2018-04-11";
    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 "2018-04-12T12:14:18Z";
    String date_modified "2019-06-03T17:25:18Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.733238.1";
    String history 
"2020-08-06T18:55:26Z (local files)
2020-08-06T18:55:26Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_733238.html";
    String infoUrl "https://www.bco-dmo.org/dataset/733238";
    String institution "BCO-DMO";
    String instruments_0_acronym "Fluorometer";
    String instruments_0_dataset_instrument_description "Used to measure chlorophyll fluorescence";
    String instruments_0_dataset_instrument_nid "733246";
    String instruments_0_description "A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/113/";
    String instruments_0_instrument_name "Fluorometer";
    String instruments_0_instrument_nid "484";
    String instruments_0_supplied_name "Walz Underwater fluorometer - Diving-PAM, Heinz Walz, Effeltrich, Germany";
    String keywords "bco, bco-dmo, biological, carbon, carbon dioxide, chemical, co2, data, dataset, date, dioxide, dmo, erddap, etr, light, management, npq, oceanography, office, pCO2, plant, Plant_ID, preliminary, rETR, tank, Tank_ID, Temp, temperature, time, trial, week, yield";
    String license "https://www.bco-dmo.org/dataset/733238/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/733238";
    String param_mapping "{'733238': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/733238/parameters";
    String people_0_affiliation "California State University Northridge";
    String people_0_affiliation_acronym "CSU-Northridge";
    String people_0_person_name "Dr Janet  E Kubler";
    String people_0_person_nid "51681";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "California State University Northridge";
    String people_1_affiliation_acronym "CSU-Northridge";
    String people_1_person_name "Dr Steve Dudgeon";
    String people_1_person_nid "51682";
    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 "Nancy Copley";
    String people_2_person_nid "50396";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "Seaweed OA Resilience";
    String projects_0_acronym "Seaweed OA Resilience";
    String projects_0_description "Benthic macroalgae contribute to intensely productive near shore  ecosystems and little is known about the potential effects of ocean  acidification on non-calcifying macroalgae. Kübler and Dudgeon will test  hypotheses about two macroalgae, Ulva spp. and Plocamium cartilagineum,  which, for different reasons, are hypothesized to be more productive  and undergo ecological expansions under predicted changes in ocean  chemistry. They have designed laboratory culture-based experiments to  quantify the scope for response to ocean acidification in Plocamium,  which relies solely on diffusive uptake of CO2, and populations of Ulva  spp., which have an inducible concentrating mechanism (CCM). The  investigators will culture these algae in media equilibrated at 8  different pCO2 levels ranging from 380 to 940 ppm to address three key  hypotheses. The first is that macroalgae (such as Plocamium  cartilagineum) that are not able to acquire inorganic carbon in changed  form will benefit, in terms of photosynthetic and growth rates, from  ocean acidification. There is little existing data to support this  common assumption. The second hypothesis is that enhanced growth of Ulva  sp. under OA will result from the energetic savings from down  regulating the CCM, rather than from enhanced photosynthesis per se.  Their approach will detect existing genetic variation for adaptive  plasticity. The third key hypothesis to be addressed in short-term  culture experiments is that there will be a significant interaction  between ocean acidification and nitrogen limited growth of Ulva spp.,  which are indicator species of eutrophication. Kübler and Dudgeon will  be able to quantify the individual effects of ocean acidification and  nitrogenous nutrient addition on Ulva spp. and also, the synergistic  effects, which will inevitably apply in many highly productive, shallow  coastal areas. The three hypotheses being addressed have been broadly  identified as urgent needs in our growing understanding of the impacts  of ocean acidification.";
    String projects_0_end_date "2016-05";
    String projects_0_geolocation "Temperate coastal waters of the USA (30 - 45 N latitude, -66 to -88 W and -117 to -125 W longitude)";
    String projects_0_name "Ocean Acidification: Scope for Resilience to Ocean Acidification in Macroalgae";
    String projects_0_project_nid "2275";
    String projects_0_start_date "2013-06";
    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 "This dataset includes photosynthetic pigment concentrations in Plocamium cartilagineum grown under various temperatures and CO2 levels, from July 2014 to February 2015. The parameters reported are: the concentrations of Chlorophyll a, Phycoerythrin, Phycocyanin, Allophycocyanin, and total Phycobiliprotein, and the ratio of total Phycobiliprotein to Chlorophyll A.";
    String title "Measurements of fluorescence of photosystem II in Plocamium cartilagineum under various and pCO2 and temperature conditions";
    String version "1";
    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.


 
ERDDAP, Version 2.02
Disclaimers | Privacy Policy | Contact