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Dataset Title:  Images of particles collected in sediment traps for quantitative analysis from
multiple platforms from 2016-2017
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_749412)
Range: longitude = -71.09866 to 151.903°E, latitude = 22.329 to 39.881332°N, time = 2015-11-04T11:03Z to 2017-02-13T17:48Z
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
 
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Cruise {
    String bcodmo_name "cruise_id";
    String description "Cruise identifier";
    String long_name "Cruise";
    String units "unitless";
  }
  Trap_Platform {
    String bcodmo_name "platform";
    String description "trap identifier";
    String long_name "Trap Platform";
    String units "unitless";
  }
  Additional_Trap_Label {
    String bcodmo_name "unknown";
    String description "additional trap label";
    String long_name "Additional Trap Label";
    String units "unitless";
  }
  Depth {
    Int16 _FillValue 32767;
    Int16 actual_range 50, 200;
    String bcodmo_name "depth_trap";
    Float64 colorBarMaximum 8000.0;
    Float64 colorBarMinimum -8000.0;
    String colorBarPalette "TopographyDepth";
    String description "depth of trap";
    String long_name "Depth";
    String standard_name "depth";
    String units "meters";
  }
  Deployment_Duration_days {
    Float32 _FillValue NaN;
    Float32 actual_range 1.042, 3.41;
    String bcodmo_name "duration";
    String description "deployment duration";
    String long_name "Deployment Duration Days";
    String units "days";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float64 _FillValue NaN;
    Float64 actual_range 22.329, 39.88133333;
    String axis "Y";
    String bcodmo_name "latitude";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "deployment latitude with positive values indicating North";
    String ioos_category "Location";
    String long_name "Latitude";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
    String source_name "Deploy_Latitude";
    String standard_name "latitude";
    String units "degrees_north";
  }
  longitude {
    String _CoordinateAxisType "Lon";
    Float64 _FillValue NaN;
    Float64 actual_range -71.09866667, 151.903;
    String axis "X";
    String bcodmo_name "longitude";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "deployment longitude with negative values indicating West";
    String ioos_category "Location";
    String long_name "Longitude";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
    String source_name "Deploy_Longitude";
    String standard_name "longitude";
    String units "degrees_east";
  }
  Deploy_Date_UTC {
    String bcodmo_name "date";
    String description "date of deployment in UTC following ISO-8601 convention";
    String long_name "Deploy Date UTC";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
    String units "unitless";
  }
  Deploy_Time_UTC {
    String bcodmo_name "time";
    String description "Time of deployment in UTC following ISO-8601 convention";
    String long_name "Deploy Time UTC";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AHMSAA01/";
    String units "unitless";
  }
  Recover_Latitude {
    Float64 _FillValue NaN;
    Float64 actual_range 21.592, 39.94433333;
    String bcodmo_name "latitude";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "recover latitude with positive values indicating North";
    String long_name "Latitude";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
    String standard_name "latitude";
    String units "decimal degrees";
  }
  Recover_Longitude {
    Float64 _FillValue NaN;
    Float64 actual_range -71.092106, 151.779;
    String bcodmo_name "longitude";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "recover longitude with negative values indicating West";
    String long_name "Longitude";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
    String standard_name "longitude";
    String units "decimal degrees";
  }
  Recover_Date_UTC {
    String bcodmo_name "date";
    String description "date of recover in UTC following ISO-8601 convention";
    String long_name "Recover Date UTC";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
    String units "unitless";
  }
  Recover_Time_UTC {
    String bcodmo_name "time";
    String description "Time of recover in UTC following ISO-8601 convention";
    String long_name "Recover Time UTC";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AHMSAA01/";
    String units "unitless";
  }
  time {
    String _CoordinateAxisType "Time";
    Float64 actual_range 1.44663498e+9, 1.48700808e+9;
    String axis "T";
    String bcodmo_name "ISO_DateTime_UTC";
    String description "deployment date and time following ISO-8901 convention";
    String ioos_category "Time";
    String long_name "Deploy Date Time";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/";
    String source_name "deploy_date_time";
    String standard_name "time";
    String time_origin "01-JAN-1970 00:00:00";
    String time_precision "1970-01-01T00:00Z";
    String units "seconds since 1970-01-01T00:00:00Z";
  }
  recover_date_time {
    String bcodmo_name "ISO_DateTime_UTC";
    String description "recover date and time following ISO-8901 convention";
    String long_name "Recover Date Time";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/";
    String time_precision "1970-01-01T00:00Z";
    String units "unitless";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
    String acquisition_description 
"The NBST carried 4 collection tubes with a diameter of 12 cm (Valdes and Price
2000). The STST included 5 frames (KC Denmark) clipped onto a surface-
tethered, free drifting array line at increasing depths and each frame carried
4, 7 cm diameter collection tubes. The WW trap consisted of one, 4-tube trap
frame (KC Denmark) tethered by a bungee below the profiling component of the
WW array.\\u00a0 To prepare tubes for deployment, seawater was collected from a
depth of 150 m using a CTD rosette and pumped through a 1 \\u03bcm filter
cartridge. Trap tubes were filled with filtered water overlying a jar
containing a polyacrylamide gel layer (Durkin et al. 2015). Trap platforms
were deployed for between 1 day and 3.5 days (see Trap Deployment Log).\\u00a0
Identically prepared tubes were incubated in parallel onboard the ship to
serve as process blanks.
 
Upon recovery, collection tubes were allowed to settle for at least 1 hour
before the overlying water was siphoned off.\\u00a0 Jars containing
polyacrylamide gel were removed from trap tubes and the remaining overlying
water was carefully pipetted off the gel.\\u00a0 Gels were stored at 4 degrees
C and imaged within the following 2 days before being stored at -80 degrees
C.\\u00a0
 
Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus
SZX16) with either a Luminera Infinity 2 (FK170124) or an Allied Vision
Technologies StingRay (EN572 and EN581) camera attachment.\\u00a0 Particles
collected in gel layers during EN572 and EN581 were imaged under brightfield
illumination.\\u00a0 Particles collected in gel layers during FK170124 were
imaged under both brightfield and oblique illumination, producing two separate
sets of images for each sample.\\u00a0 EN572 gel layers were imaged with a
transparent grid to assist in tracking gel location during imaging. The grid
was not used when imaging samples collected during subsequent cruises because
the pronounced grid lines complicated image analysis. All gel layers were
imaged at 4 increasing magnifications, though the combination of
magnifications varied by cruise: at 7x, 20x, 40x, and 115x for EN572 samples,
at 7x, 20x, 40x, and 80x for EN581 samples, and at 7x, 20x, 50x, and 115x for
FK170124 samples. At magnifications greater than 7x, multiple focal planes
within a field of view were imaged to capture particles embedded in different
depths of the gel layer.\\u00a0 The number of focal planes imaged was
consistent across all fields of view for a given magnification but varied
across cruises due to variation in gel thickness and particle types present.
To determine whether measured particle properties changed if gel layers are
frozen, samples collected during FK170124 were thawed after being stored for
approximately 1 year at -80\\u00a0 degrees C and imaged again under both
brightfield and oblique illumination.";
    String awards_0_award_nid "675295";
    String awards_0_award_number "OCE-1703664";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1703664";
    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 
"Images of particles collected in sediment traps for quantitative analysis from multiple platforms from 2016-2017 
  PI: Colleen Durkin 
  Version: 2019-10-18";
    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 "2018-11-07T17:55:41Z";
    String date_modified "2020-07-15T15:47:38Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.26008/1912/bco-dmo.749412.1";
    Float64 Easternmost_Easting 151.903;
    Float64 geospatial_lat_max 39.88133333;
    Float64 geospatial_lat_min 22.329;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max 151.903;
    Float64 geospatial_lon_min -71.09866667;
    String geospatial_lon_units "degrees_east";
    String history 
"2020-09-28T14:23:36Z (local files)
2020-09-28T14:23:36Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_749412.das";
    String infoUrl "https://www.bco-dmo.org/dataset/749412";
    String institution "BCO-DMO";
    String instruments_0_acronym "camera";
    String instruments_0_dataset_instrument_description "Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16) with either a Luminera Infinity 2 (FK170124) or an Allied Vision Technologies StingRay (EN572 and EN581) camera attachment.";
    String instruments_0_dataset_instrument_nid "749428";
    String instruments_0_description "All types of photographic equipment including stills, video, film and digital systems.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/311/";
    String instruments_0_instrument_name "Camera";
    String instruments_0_instrument_nid "520";
    String instruments_0_supplied_name "Luminera Infinity 2 microscope camera";
    String instruments_1_dataset_instrument_description "Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16)";
    String instruments_1_dataset_instrument_nid "749427";
    String instruments_1_description "Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a \"light microscope\".";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB05/";
    String instruments_1_instrument_name "Microscope-Optical";
    String instruments_1_instrument_nid "708";
    String instruments_1_supplied_name "Olympus SZX16 Stereomicroscope";
    String keywords "additional, Additional_Trap_Label, bco, bco-dmo, biological, chemical, cruise, data, dataset, date, days, deploy, Deploy_Date_UTC, Deploy_Time_UTC, deployment, Deployment_Duration_days, depth, dmo, duration, erddap, label, latitude, longitude, management, oceanography, office, platform, preliminary, recover, recover_date_time, Recover_Date_UTC, Recover_Latitude, Recover_Longitude, Recover_Time_UTC, time, trap, Trap_Platform";
    String license "https://www.bco-dmo.org/dataset/749412/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/749412";
    Float64 Northernmost_Northing 39.88133333;
    String param_mapping "{'749412': {'Deploy_Latitude': 'flag - latitude', 'deploy_date_time': 'flag - time', 'Deploy_Longitude': 'flag - longitude'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/749412/parameters";
    String people_0_affiliation "Moss Landing Marine Laboratories";
    String people_0_affiliation_acronym "MLML";
    String people_0_person_name "Colleen Durkin";
    String people_0_person_nid "675299";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Skidmore College";
    String people_1_person_name "Margaret L. Estapa";
    String people_1_person_nid "644830";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "University of Rhode Island";
    String people_2_affiliation_acronym "URI-GSO";
    String people_2_person_name "Melissa Omand";
    String people_2_person_nid "675309";
    String people_2_role "Co-Principal Investigator";
    String people_2_role_type "originator";
    String people_3_affiliation "Woods Hole Oceanographic Institution";
    String people_3_affiliation_acronym "WHOI BCO-DMO";
    String people_3_person_name "Mathew Biddle";
    String people_3_person_nid "708682";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "EAGER DNA BioPump";
    String projects_0_acronym "EAGER DNA BioPump";
    String projects_0_description 
"Text from the NSF award abstract:
Carbon is fixed into organic matter by phytoplankton growing in the surface ocean, and is naturally sequestered in the ocean interior when particles and organisms sink: a process called the \"biological pump.\" Because of its recognized influence on the global carbon cycle, ocean scientists have studied the biological pump for decades. However, we still do not have a sufficient understanding of the underlying processes to accurately quantify and predict carbon cycling. Much of this uncertainty stems from an inability to directly link specific plankton in the surface ocean with the types of particles sinking out of the surface ocean. To address this missing link in biological pump research, this work will directly observe how plankton are transported out of the surface ocean using novel, particle-specific observational approaches embedded within an interdisciplinary field program that will finely resolve upper ocean plankton groups and the resulting amount of sinking carbon across space and in time. The genetic identity of organisms within different types of sinking particles will be determined by sequencing the genetic contents of individually collected particles. This new application of a molecular method will definitively link surface plankton with sinking particles at five locations across the Pacific Ocean. This work has the potential to transform our understanding of the biological pump by identifying previously unknown links between surface ecosystems and sinking carbon particles. Because this work is embedded within an interdisciplinary field program, including biogeochemical modelers and remote sensing scientists, these data will feed directly into new models of the biological pump, improving our ability to quantify and predict carbon uptake by the ocean. This project will train 1 graduate student and at least 2 undergraduate researchers. Findings will be communicated to the non-scientific public through blogs, videos, and the public communication channels of participating institutions.
Accurate prediction of the global carbon cycle requires an understanding of the specific processes that link surface plankton communities and sinking particulate carbon flux (export) out of the surface ocean, but current methodological paradigms in biological pump research do not directly observe these processes. This project will comprehensively determine who is exported from the surface ocean and how using new, particle-resolving optical and molecular techniques embedded within a sampling scheme that characterizes export events at high time and space resolution. The investigation suggests that different plankton types in the surface waters are transported out of the surface ocean by distinct export pathways, and that an understanding of these connections is critical knowledge for global carbon cycle modeling. If successful, this work has the potential to transform our conceptual understanding of the biological pump by directly identifying mechanisms that link surface plankton with particle export, without relying on bulk sampling schemes and large-scale correlation analysis. Particle export environments will be studied at five open ocean locations during a cruise from Hawaii to Seattle in January-February 2017. The surface plankton communities will be characterized by a combination of satellite observations, sensors attached to a free-drifting, continuously profiling WireWalker, an in situ holographic camera, microscopy, and by sequencing 18S and 16S rRNA gene fragments. Exported particles will simultaneously be captured by various specialized sediment traps and their characteristics will be directly related to their sources in the surface community by identifying the genetic contents of individual particle types. Individual particles will be isolated from gel layers and the 16S and 18S rRNA gene fragments will be amplified and sequenced. This work would, for the first time, combine molecular approaches with particle-specific observations to enable simultaneous identification of both which organisms are exported and the processes responsible for their export.";
    String projects_0_end_date "2018-11";
    String projects_0_geolocation "Eastern Pacific";
    String projects_0_name "Collaborative Research: EAGER: Particle-specific DNA sequencing to directly observe ecological mechanisms of the biological pump";
    String projects_0_project_nid "675296";
    String projects_0_start_date "2016-12";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 22.329;
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "Images of particles collected in sediment traps for quantitative analysis from multiple platforms from 2016-2017";
    String time_coverage_end "2017-02-13T17:48Z";
    String time_coverage_start "2015-11-04T11:03Z";
    String title "Images of particles collected in sediment traps for quantitative analysis from multiple platforms from 2016-2017";
    String version "1";
    Float64 Westernmost_Easting -71.09866667;
    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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