Accessing BCO-DMO data
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Dataset Title:  Raw benthic chlorophyll and phaeophytin data from cores collected in
Massachusetts from 2012-2015.
Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_669652)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Files | Make a graph
Variable ?   Optional
Constraint #1 ?
Constraint #2 ?
   Minimum ?
   Maximum ?
 month (unitless) ?          6    10
 estuary (unitless) ?              
 plot (unitless) ?              
 timepoint (unitless) ?              
 experiment (unitless) ?              
 sampleID (unitless) ?              
 chla (ug cm-2) ?          0.63    17.69
 phaeo (ug cm-2) ?          2.01    42.78
 logchla (log) ?          -0.2    1.25
 logphaeo (log) ?          0.3    1.63
 chla_phaeo (ug cm-2) ?          0.289389068    0.413556109
Server-side Functions ?
 distinct() ?
? (" ")

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 {
  month {
    Byte _FillValue 127;
    Byte actual_range 6, 10;
    String description "Samping month; mm";
    String ioos_category "Time";
    String long_name "Month";
    String units "unitless";
  estuary {
    String description "Estuary where sampling occurred";
    String ioos_category "Unknown";
    String long_name "Estuary";
    String units "unitless";
  plot {
    String description "Plot ID";
    String ioos_category "Unknown";
    String long_name "Plot";
    String units "unitless";
  timepoint {
    String description "Timepoint refers to when the sample was collected before (PL) or after the 13C-isotope label was added";
    String ioos_category "Time";
    String long_name "Timepoint";
    String units "unitless";
  experiment {
    String description "Experiment refers to whether the 13C label was applied as benthic microalgae (BMA) or Spartina alterniflora (salt) detritus.";
    String ioos_category "Unknown";
    String long_name "Experiment";
    String units "unitless";
  sampleID {
    String description "Sample ID number";
    String ioos_category "Identifier";
    String long_name "Sample ID";
    String units "unitless";
  chla {
    Float32 _FillValue NaN;
    Float32 actual_range 0.63, 17.69;
    Float64 colorBarMaximum 30.0;
    Float64 colorBarMinimum 0.03;
    String colorBarScale "Log";
    String description "Benthic chlorophyll concentration";
    String ioos_category "Ocean Color";
    String long_name "Concentration Of Chlorophyll In Sea Water";
    String units "ug cm-2";
  phaeo {
    Float32 _FillValue NaN;
    Float32 actual_range 2.01, 42.78;
    String description "Phaeophytin concentration";
    String ioos_category "Unknown";
    String long_name "Phaeo";
    String units "ug cm-2";
  logchla {
    Float32 _FillValue NaN;
    Float32 actual_range -0.2, 1.25;
    String description "Log 10 benthic chlorophyll concentration";
    String ioos_category "Ocean Color";
    String long_name "Logchla";
    String units "log";
  logphaeo {
    Float32 _FillValue NaN;
    Float32 actual_range 0.3, 1.63;
    String description "Log 10 phaeophytin concentration";
    String ioos_category "Unknown";
    String long_name "Logphaeo";
    String units "log";
  chla_phaeo {
    Float64 _FillValue NaN;
    Float64 actual_range 0.289389068, 0.413556109;
    Float64 colorBarMaximum 30.0;
    Float64 colorBarMinimum 0.03;
    String colorBarScale "Log";
    String description "Ratio of chlorphyll to phaeophytin concentrations";
    String ioos_category "Ocean Color";
    String long_name "Concentration Of Chlorophyll In Sea Water";
    String units "ug cm-2";
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Sediment samples for organic matter composition were collected by placing a
hard plastic sleeve around a polyvinyl chloride (PVC)\\u00a0corer\\u00a0(5 cm
diameter x 15 cm deep) and then removing the\\u00a0corer. The plastic sleeve
remained in place to maintain the integrity of the sediment column and mark
the core location (Spivak 2015). The top 0.5 cm of each core was collected
into pre-combusted vials and frozen (-80 deg C) until analysis for total
organic carbon and nitrogen content and stable isotopes (d13C, d15N) and lipid
biomarker composition. Adjacent samples for benthic chlorophyll were collected
with smaller cores (1.5 cm diameter x 1 cm deep) into glass vials and frozen
(-20 deg C) until analysis. Additional sediment cores for organic matter
composition and benthic chlorophyll were collected 4, 8, 24, and 48 h after
the\\u00a013C-labeled NaHCO3\\u00a0was applied in June, August, and October and
4, 8, 24, and 144h after the\\u00a013C-
labeled\\u00a0S.\\u00a0alterniflora\\u00a0was applied in August.\\u00a0 Benthic
chlorophyll was determined per methods described by Neubauer et al. (2000).
Spivak, AC and J Ossolinski. 2016. Limited effects of nutrient enrichment on
bacterial carbon sources in salt marsh tidal creek sediments. Marine Ecology
Progress Series. 544:107-130.10.3354/meps11587";
    String awards_0_award_nid "529582";
    String awards_0_award_number "OCE-1233678";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1233678";
    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 "Dr David  L. Garrison";
    String awards_0_program_manager_nid "50534";
    String cdm_data_type "Other";
    String comment 
"Sediment Chlorophyll Data 
  Amanda Spivak, PI 
  Version 8 December 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 2.2d  13 Jun 2019";
    String date_created "2016-12-10T00:39:31Z";
    String date_modified "2019-04-05T17:26:53Z";
    String defaultDataQuery "&time";
    String doi "10.1575/1912/bco-dmo.669652.1";
    String history 
"2019-09-18T11:10:45Z (local files)
2019-09-18T11:10:45Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_669652.html";
    String infoUrl "https://www.bco-dmo.org/dataset/669652";
    String institution "BCO-DMO";
    String instruments_0_dataset_instrument_description "Used to collect core samples";
    String instruments_0_dataset_instrument_nid "669658";
    String instruments_0_description 
"Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.

Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/";
    String instruments_0_instrument_name "Push Corer";
    String instruments_0_instrument_nid "628287";
    String instruments_0_supplied_name "Core";
    String keywords "bco, bco-dmo, biological, chemical, chemistry, chla, chla_phaeo, chlorophyll, chlorophyll-a, color, concentration, concentration_of_chlorophyll_in_sea_water, data, dataset, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Chlorophyll, erddap, estuary, experiment, identifier, logchla, logphaeo, management, month, ocean, ocean color, oceanography, oceans, office, phaeo, plot, preliminary, sample, sampleID, science, sea, seawater, time, timepoint, water";
    String keywords_vocabulary "GCMD Science Keywords";
    String license 
"The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.";
    String metadata_source "https://www.bco-dmo.org/api/dataset/669652";
    String param_mapping "{'669652': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/669652/parameters";
    String people_0_affiliation "Woods Hole Oceanographic Institution";
    String people_0_affiliation_acronym "WHOI";
    String people_0_person_name "Amanda Spivak";
    String people_0_person_nid "529580";
    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 BCO-DMO";
    String people_1_person_name "Hannah Ake";
    String people_1_person_nid "650173";
    String people_1_role "BCO-DMO Data Manager";
    String people_1_role_type "related";
    String project "Eutrophication Effects on Sediment Metabolism and Benthic Algal-bacterial Coupling: An Application of Novel Techniques in a LTER Estuary";
    String projects_0_acronym "benthic_PP_at_TIDE";
    String projects_0_description 
"Extracted from the NSF award abstract:
This project will address how rates of benthic microalgal production respond to eutrophication and geomorphological changes in human-impacted tidal creeks. Excess nutrient loading increases benthic algal biomass and likely stimulates production rates but the magnitude of nutrient and geomorphological effects on rates of production is unknown. Will changes in benthic algal productivity affect algal-bacterial coupling? Furthermore, how is algal-bacterial coupling affected by geomorphological changes, which may be exacerbated by excess nutrient loading but can also occur in pristine marshes?
This project will take advantage of the infrastructure of the TIDE project, a long-term saltmarsh eutrophication experiment at the Plum Island Ecosystem - Long Term Ecological Research site in Northeastern Massachusetts. Specifically, the PIs will measure benthic metabolism and examine algal- bacterial coupling in fertilized and ambient nutrient tidal creeks in the first field season. The following field season, they will compare sediment metabolism and carbon dynamics on slumped tidal creek walls (i.e. areas where low marsh has collapsed into the tidal creek) to that on the bottom of tidal creeks. In both years, gross and net production will be determined using an innovative triple oxygen isotope technique and traditional dissolved oxygen and inorganic carbon flux measurements. Comparisons between these methods will be useful in informing studies of sediment metabolism. Lipid biomarkers will be used to characterize the sources of organic matter to creek sediments, and stable isotope analysis of bacterial specific biomarkers to identify the sources of organic carbon utilized by sediment bacteria. The biomarkers will reveal whether sediment bacteria use organic matter substrates, such as benthic microalgal carbon, selectively or in proportion to availability. Overall, results from the proposed study will provide important information about how sediment carbon dynamics in shallow tidal creeks respond to long term eutrophication. Furthermore, findings will enhance understanding of the role of tidal creeks in coastal biogeochemistry.";
    String projects_0_end_date "2015-08";
    String projects_0_geolocation "Plum Island Estuary, Rowley Massachusetts";
    String projects_0_name "Eutrophication Effects on Sediment Metabolism and Benthic Algal-bacterial Coupling: An Application of Novel Techniques in a LTER Estuary";
    String projects_0_project_nid "529583";
    String projects_0_start_date "2012-09";
    String publisher_name "Hannah Ake";
    String publisher_role "BCO-DMO Data Manager(s)";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v29";
    String summary "Raw benthic chlorophyll and phaeophytin data from cores collected in Massachusetts from 2012-2015.";
    String title "Raw benthic chlorophyll and phaeophytin data from cores collected in Massachusetts from 2012-2015.";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.5-beta";


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
For example,
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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