Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | [CTD_CH0112] - CTD data from 39 stations from R/V Cape Hatteras cruise CH0112 in the Northwest Atlantic Continental Shelf in 2012 (CiliateSequencing project) (Diversity and dynamics of planktonic ciliates - what can next- generation sequencing technologies tell us?) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_3959) |
| Information: | Summary
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| FGDC
| ISO 19115
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Attributes {
s {
sta {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 39;
String bcodmo_name "sta";
String description "Station ID number.";
String long_name "Sta";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 39.7763, 41.2477;
String axis "Y";
String bcodmo_name "lat_start";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude at start of CTD cast. North = positive.";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String source_name "lat_start";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -71.4673, -71.4587;
String axis "X";
String bcodmo_name "lon_start";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude at start of CTD cast. West = negative.";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String source_name "lon_start";
String standard_name "longitude";
String units "degrees_east";
}
month_start {
String bcodmo_name "month_start";
String description "2-digit month at start of cast.";
String long_name "Month Start";
String units "mm (01 to 12)";
}
day_start {
String bcodmo_name "day_start";
String description "2-digit day of month at start of cast.";
String long_name "Day Start";
String units "dd (01 to 31)";
}
year {
Int16 _FillValue 32767;
Int16 actual_range 2012, 2012;
String bcodmo_name "year";
String description "4-digit year in YYYY format.";
String long_name "Year";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "unitless";
}
time_start {
String bcodmo_name "time_start";
String description "Time at start of cast (UTC).";
String long_name "Time Start";
String units "HHMM.mm";
}
time {
String _CoordinateAxisType "Time";
Float64 actual_range 1.341613157e+9, 1.341831262e+9;
String axis "T";
String bcodmo_name "ISO_DateTime_UTC";
String description "Date/time (UTC) at start of cast formatted to ISO 8601 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 source_name "ISO_DateTime_UTC";
String standard_name "time";
String time_origin "01-JAN-1970 00:00:00";
String time_precision "1970-01-01T00:00:00Z";
String units "seconds since 1970-01-01T00:00:00Z";
}
press {
Float32 _FillValue NaN;
Float32 actual_range 1.546, 861.284;
String bcodmo_name "pressure";
String description "Pressure";
String long_name "Press";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PRESPR01/";
String units "decibars";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 1.534, 852.931;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Depth";
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";
}
cond {
Float32 _FillValue NaN;
Float32 actual_range 0.006806, 5.082737;
String bcodmo_name "conductivity";
String description "Conductivity in Siemens per meter.";
String long_name "Cond";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/CNDC/";
String units "S/m";
}
temp {
Float32 _FillValue NaN;
Float32 actual_range 4.7069, 24.8754;
String bcodmo_name "temperature";
String description "Temperature (degrees Celsius) from primary sensor.";
String long_name "Temperature";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/";
String units "degrees C";
}
temp2 {
Float32 _FillValue NaN;
Float32 actual_range 4.7051, 25.0675;
String bcodmo_name "temp2";
String description "Temperature (degrees Celsius) from secondary sensor.";
String long_name "Temp2";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPS601/";
String units "degrees C";
}
fluor {
Float32 _FillValue NaN;
Float32 actual_range 0.0059, 1.6435;
String bcodmo_name "fluorescence";
String description "Chlorophyll fluorescence (micrograms per liter) measured by Chelsea Aqua 3 sensor. Fluorescence values should be interpreted as \"arbitrary units\" because calibrations have not been applied.";
String long_name "Fluor";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/CPHLPM01/";
String units "ug/L";
}
O2 {
Float32 _FillValue NaN;
Float32 actual_range 4.15016, 10.49208;
String bcodmo_name "Dissolved_Oxygen";
String description "Oxygen (milligrams per liter) measured by SBE 43 sensor.";
String long_name "O2";
String units "mg/L";
}
scan {
Int16 _FillValue 32767;
Int16 actual_range 1, 27611;
String bcodmo_name "scan";
String description "CTD scan number.";
String long_name "Scan";
String units "integer";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson,.odvTxt";
String acquisition_description
"23 stations were sampled along a transect from Narragansett, RI to the shelf
break. 16 stations were sampled on the way back.
\\---------------------------------------------
Header information from CTD files:
Sea-Bird SBE 9 Data File:
Software Version Seasave V 7.20a
Temperature SN = 0967
Conductivity SN = 0626
Number of Bytes Per Scan = 41
Number of Voltage Words = 4
Number of Scans Averaged by the Deck Unit = 1
Append System Time to Every Scan
---------------------------------------------";
String awards_0_award_nid "54721";
String awards_0_award_number "OCE-1129734";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1129734";
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 awards_1_award_nid "54820";
String awards_1_award_number "OCE-1130033";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1130033";
String awards_1_funder_name "NSF Division of Ocean Sciences";
String awards_1_funding_acronym "NSF OCE";
String awards_1_funding_source_nid "355";
String awards_1_program_manager "David L. Garrison";
String awards_1_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"CTD Data from CH0112 Cruise
R/V Hatteras - July 06-09, 2012
PI: George B. McManus (UConn)
Co-PI: Laura A. Katz (Smith College)
Version: 07 June 2013";
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 "2013-06-07T17:07:46Z";
String date_modified "2019-11-06T17:07:26Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.3959.1";
Float64 Easternmost_Easting -71.4587;
Float64 geospatial_lat_max 41.2477;
Float64 geospatial_lat_min 39.7763;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -71.4587;
Float64 geospatial_lon_min -71.4673;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 852.931;
Float64 geospatial_vertical_min 1.534;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-12-23T03:25:33Z (local files)
2024-12-23T03:25:33Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_3959.html";
String infoUrl "https://www.bco-dmo.org/dataset/3959";
String institution "BCO-DMO";
String instruments_0_acronym "CTD SBE 9";
String instruments_0_dataset_instrument_nid "6179";
String instruments_0_description "The Sea-Bird SBE 9 is a type of CTD instrument package. The SBE 9 is the Underwater Unit and is most often combined with the SBE 11 Deck Unit (for real-time readout using conductive wire) when deployed from a research vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorometer, altimeter, etc.). Note that in most cases, it is more accurate to specify SBE 911 than SBE 9 since it is likely a SBE 11 deck unit was used. more information from Sea-Bird Electronics";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/130/";
String instruments_0_instrument_name "CTD Sea-Bird 9";
String instruments_0_instrument_nid "488";
String instruments_0_supplied_name "CTD Sea-Bird 9";
String keywords "bco, bco-dmo, biological, chemical, cond, data, dataset, date, day, day_start, depth, dmo, erddap, fluor, iso, latitude, longitude, management, month, month_start, O2, oceanography, office, oxygen, preliminary, press, scan, sta, start, temp2, temperature, time, time_start, year";
String license "https://www.bco-dmo.org/dataset/3959/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/3959";
Float64 Northernmost_Northing 41.2477;
String param_mapping "{'3959': {'depth': 'flag - depth', 'lon_start': 'flag - longitude', 'ISO_DateTime_UTC': 'master - time', 'lat_start': 'flag - latitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/3959/parameters";
String people_0_affiliation "University of Connecticut";
String people_0_affiliation_acronym "UConn - Avery Point";
String people_0_person_name "George B. McManus";
String people_0_person_nid "51375";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Smith College";
String people_1_person_name "Laura A. Katz";
String people_1_person_nid "51376";
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 "Shannon Rauch";
String people_2_person_nid "51498";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "CiliateSequencing";
String projects_0_acronym "CiliateSequencing";
String projects_0_description
"The Ocean's biomass and diversity are predominantly microbial, yet this aspect of diversity remains underexplored. Efforts in recent years have begun to document microbial diversity in marine systems, and to elucidate the processes that structure assemblages across space and time. This project focuses on two important sister clades of microbial eukaryotes, the oligotrich and choreotrich ciliates. These organisms comprise a major component of planktonic food webs as they graze on phytoplankton, and are in turn eaten by zooplankton and larval fish.
Earlier molecular work on ciliate diversity relied on light microscopy, construction of clone libraries and Sanger sequencing. This revealed a high degree of cryptic diversity (similar species that are genetically distinct), which is surprising, given the long-held idea that all microbes are globally distributed and that few species exist, at least as compared to animals and plants. This past work also showed that ciliate assemblages contain a few highly abundant forms and many rare ones, consistent with the concept of a \"rare biosphere\". However, these methods are limited by high costs of both labor and materials, so that efforts to sample any local assemblage comprehensively usually resulted in undersaturation (repeated sampling continued to uncover new species). Next generation approaches are needed to truly assess the depths of biodiversity in planktonic ciliates.
This project brings together investigators with strengths in ecology, taxonomy and oceanography (PI McManus) and in molecular evolution, systematics and bioinformatics (PI Katz). Pyrosequencing will be used to sample the oligotrich and choreotrich ciliates ’to exhaustion’ in coastal environments. Denaturing gradient gel electrophoresis (DGGE), a technique that generates a fingerprint of the diversity in a sample, will be used to pre-select samples for pyrosequencing based on where strong gradients are observed in the composition of assemblages in relation to environmental factors (density fronts, thermolclines, etc.). Using these approaches, combined with the informatics pipeline already in place, this project will address three specific objectives:
Objective 1. Determine the spatial scale of variability in ciliate diversity by measuring how ciliate assemblages change over meter, kilometer, 100 km, and basin scales.
Objective 2. Assess the contributions of different size classes of ciliates to overall assemblage diversity.
Objective 3. Experimentally evaluate factors that control the temporal shift of individual species from rarity to commonness in a natural assemblage, and vice versa.
Note: See the related collaborative project, \"Patterns of diversity in planktonic ciliates: spatio-temporal scales and community assembly in the coastal ocean\", funded by awards OCE-1435515 and OCE-1436003.";
String projects_0_end_date "2015-08";
String projects_0_geolocation "NW Atlantic Continental Shelf";
String projects_0_name "Diversity and dynamics of planktonic ciliates - what can next-generation sequencing technologies tell us?";
String projects_0_project_nid "2164";
String projects_0_project_website "http://microzooplankton.uconn.edu";
String projects_0_start_date "2012-07";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 39.7763;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "month_start,year";
String summary "CTD data from 39 stations from R/V Cape Hatteras cruise CH0112 in the Northwest Atlantic Continental Shelf in 2012.";
String time_coverage_end "2012-07-09T10:54:22Z";
String time_coverage_start "2012-07-06T22:19:17Z";
String title "[CTD_CH0112] - CTD data from 39 stations from R/V Cape Hatteras cruise CH0112 in the Northwest Atlantic Continental Shelf in 2012 (CiliateSequencing project) (Diversity and dynamics of planktonic ciliates - what can next-generation sequencing technologies tell us?)";
String version "1";
Float64 Westernmost_Easting -71.4673;
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
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.