Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | [Salp sample log] - Salp specimen log for genomic and transcriptomic study collected from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project) (Population ecology of Salpa thompsoni based on molecular indicators) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_672600) |
| Information: | Summary
| License
| FGDC
| ISO 19115
| Metadata
| Background
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Attributes {
s {
cruise_id {
String bcodmo_name "cruise_id";
String description "cruise identifier";
String long_name "Cruise Id";
String units "unitless";
}
region {
String bcodmo_name "region";
String description "region of Southern Ocean";
String long_name "Region";
String units "unitless";
}
season {
String bcodmo_name "season";
String description "season and year of collection";
String long_name "Season";
String units "unitless";
}
area {
String bcodmo_name "region";
String description "area within region of Southern Ocean";
String long_name "Area";
String units "unitless";
}
station {
Int16 _FillValue 32767;
Int16 actual_range 4, 184;
String bcodmo_name "station";
String description "station number";
String long_name "Station";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range -66.183, -60.901;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "latitude; north is positive";
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 -74.567, 42.002;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "longitude; east is positive";
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";
}
num_samples {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 4, 5;
String bcodmo_name "count";
String description "number of samples collected";
String long_name "Num Samples";
String units "unitless";
}
temp {
Float32 _FillValue NaN;
Float32 actual_range -1.28, 1.28;
String bcodmo_name "temperature";
String description "temperature";
String long_name "Temperature";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/";
String units "degrees Celsius";
}
sal {
Float32 _FillValue NaN;
Float32 actual_range 33.39, 34.6;
String bcodmo_name "sal";
String description "salinity";
String long_name "Sal";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/";
String units "PPT";
}
depth_range {
String bcodmo_name "depth_range";
String description "sampled depth";
String long_name "Depth";
String standard_name "depth";
String units "meters";
}
depth_w {
Int16 _FillValue 32767;
Int16 actual_range 452, 4300;
String bcodmo_name "depth_w";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "water column depth";
String long_name "Depth";
String standard_name "depth";
String units "meters";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"1) Cruise R/V LM GOULD (LMG1110): Samples collected using Multiple
Opening/Closing Net and Environmental Sensing System (MOCNESS) with a mouth
opening of 1-m2 and nine 335\\u03bcm mesh nets; upper 200 m were sampled with a
2.3 m2 Isaacs-Kidd Midwater Trawl (IKMT) with a 505 \\u00b5m mesh
net.\\u00a0Western Antarctic Peninsula region, Southern Ocean (November-
December 2011)
2) Cruise\\u00a0R/V Polarstern (PS-ANT-XVII/2): Samples collected using a
Rectangular Midwater Trawl (RMT 1+8) from the upper 200 m.\\u00a0Western
Antarctic Peninsula region, Southern Ocean (January 2011)
3) Cruise R/V Umitaka Maru (UM-08-09): Samples collected using a RMT 1+8 from
2,000 m to surface. Indian Sector, Southern Ocean (January 2009)";
String awards_0_award_nid "54892";
String awards_0_award_number "ANT-1044982";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1044982";
String awards_0_funder_name "NSF Antarctic Sciences";
String awards_0_funding_acronym "NSF ANT";
String awards_0_funding_source_nid "369";
String awards_0_program_manager "Dr Peter Milne";
String awards_0_program_manager_nid "51468";
String cdm_data_type "Other";
String comment
"Salpa thompsoni collection information
PI: A. Bucklin (UConn)
version: 2017-01-06
NOTE: These data were published in Table 1, Batta-Lona et al (2016) Pol. Bio. doi:10.1007/s00300-016-2051-6";
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 "2017-01-06T19:21:21Z";
String date_modified "2018-10-03T18:16:40Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.728220";
Float64 Easternmost_Easting 42.002;
Float64 geospatial_lat_max -60.901;
Float64 geospatial_lat_min -66.183;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max 42.002;
Float64 geospatial_lon_min -74.567;
String geospatial_lon_units "degrees_east";
String history
"2024-11-21T12:05:58Z (local files)
2024-11-21T12:05:58Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_672600.html";
String infoUrl "https://www.bco-dmo.org/dataset/672600";
String institution "BCO-DMO";
String instruments_0_acronym "MOC1";
String instruments_0_dataset_instrument_nid "674089";
String instruments_0_description "The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. The MOCNESS-1 carries nine 1-m2 nets usually of 335 micrometer mesh and is intended for use with the macrozooplankton. All nets are black to reduce contrast with the background. A motor/toggle release assembly is mounted on the top portion of the frame and stainless steel cables with swaged fittings are used to attach the net bar to the toggle release. A stepping motor in a pressure compensated case filled with oil turns the escapement crankshaft of the toggle release which sequentially releases the nets to an open then closed position on command from the surface. -- from the MOCNESS Operations Manual (1999 + 2003).";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/NETT0097/";
String instruments_0_instrument_name "MOCNESS1";
String instruments_0_instrument_nid "437";
String instruments_0_supplied_name "Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) with a mouth opening of 1-m2 and nine 335μm mesh nets";
String instruments_1_acronym "TrawlMid";
String instruments_1_dataset_instrument_nid "674090";
String instruments_1_description
"A mid-water or pelagic trawl is a net towed at a chosen depth in the water column to catch schooling fish such as herring and mackerel. Midwater trawl nets have very large front openings to herd schooling fish toward the back end where they become trapped in the narrow \"broiler\". The sides of the deployed net are spread horizontally with two large metal foils, called \"doors,\" positioned in front of the net. As the trawler moves forward, the doors, and therefore the net, are forced outward, keeping the net open.
This instrument designation is used when specific make and model are not known.";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/23/";
String instruments_1_instrument_name "Midwater Trawl";
String instruments_1_instrument_nid "467";
String instruments_1_supplied_name "Rectangular Midwater Trawl (RMT 1+8)";
String instruments_2_acronym "IKMT";
String instruments_2_dataset_instrument_nid "674091";
String instruments_2_description
"A trawl with a pentagonal mouth opening and a dihedral depressor vane as part of the mouth opening. IKMTs come in various dimensions (refer to individual dataset documentation).
The original IKMTs were 10 foot (304 cm) and 15 foot (457 cm) at the mouth. The 10 foot IKMT net was 31 feet (9.45 m) in length (Wiebe and Benfield 2003).";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L22/current/NETT0071/";
String instruments_2_instrument_name "Isaacs-Kidd Midwater Trawl";
String instruments_2_instrument_nid "715";
String instruments_2_supplied_name "2.3 m2 Isaacs-Kidd Midwater Trawl (IKMT) with a 505 µm mesh net";
String keywords "altimetry, area, bco, bco-dmo, biological, chemical, cruise, cruise_id, data, dataset, depth, depth_range, depth_w, dmo, erddap, laboratory, latitude, longitude, management, num, num_samples, oceanography, office, preliminary, region, sal, samples, satellite, season, station, temperature";
String license "https://www.bco-dmo.org/dataset/672600/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/672600";
Float64 Northernmost_Northing -60.901;
String param_mapping "{'672600': {'lat': 'master - latitude', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/672600/parameters";
String people_0_affiliation "University of Connecticut";
String people_0_affiliation_acronym "UConn - Avery Point";
String people_0_person_name "Ann Bucklin";
String people_0_person_nid "50389";
String people_0_role "Chief Scientist";
String people_0_role_type "originator";
String people_1_affiliation "University of Connecticut";
String people_1_affiliation_acronym "UConn - Avery Point";
String people_1_person_name "Ann Bucklin";
String people_1_person_nid "50389";
String people_1_role "Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "University of Connecticut";
String people_2_affiliation_acronym "UConn";
String people_2_person_name "Dr Rachel J. O'Neill";
String people_2_person_nid "51393";
String people_2_role "Co-Principal Investigator";
String people_2_role_type "originator";
String people_3_affiliation "Connecticut Sea Grant";
String people_3_affiliation_acronym "CTSG";
String people_3_person_name "Dr Diana Payne";
String people_3_person_nid "51392";
String people_3_role "Co-Principal Investigator";
String people_3_role_type "originator";
String people_4_affiliation "Woods Hole Oceanographic Institution";
String people_4_affiliation_acronym "WHOI BCO-DMO";
String people_4_person_name "Nancy Copley";
String people_4_person_nid "50396";
String people_4_role "BCO-DMO Data Manager";
String people_4_role_type "related";
String project "Salp_Antarctic";
String projects_0_acronym "Salp_Antarctic";
String projects_0_description
"The Antarctic salp, Salpa thompsoni, is an increasingly important player in the vulnerable Antarctic Peninsula pelagic ecosystem. Observations of high abundance of Salpa thompsoni during the summer in the Southern Ocean suggest that this species is capable of rapid somatic and population growth, and frequently forms dense blooms under favorable environmental conditions. The proposed research will examine genome-wide patterns of gene expression, target gene expression levels, and patterns of population genetic diversity and structure of the target salp species. Our preliminary results and data analysis have provided a promising basis for transcriptomic studies of S. thompsoni in the Southern Ocean. The proposed next steps in our genomic/transcriptomic analysis of Salpa thompsoni are: 1) completion of a reference transcriptome as a basis for genome-wide analysis of gene expression; 2) whole transcriptome shotgun sequencing (RNA-Seq) analysis to characterize gene expression in relation to individual characteristics and environmental conditions; 3) quantitative real-time PCR (qRT-PCR) characterization and validation of gene expression for 10-20 top differentially-expressed genes; and 4) detection of strand-specific allelic variation at SNP (Single Nucleotide Polymorphic) sites to analyze clonal diversity and population genetic diversity and structure. We hypothesize that: 1) deep analysis of the Salpa thompsoni transcriptome will reveal significant associations among selected set of differentially-expressed genes and critical life history stages and events (e.g., ontogenetic maturation, sexual reproduction, senescence) of the salp; and 2) the species will show variable levels of clonal diversity and significant genetic differentiation among salp populations in different regions of the Southern Ocean. Samples will be obtained from research cruises during 2011-2013 in diverse regions of the Southern Ocean; dedicated sample and data collection will be carried out during a cruise of the R/V LM GOULD (LMG11-10) to the Western Antarctic Peninsula region in November, 2011. The significance of this effort lies in new understanding of the molecular processes underlying the complex life history and population dynamics of S. thompsoni in relation to the Antarctic pelagic ecosystem and extreme and variable environmental conditions of the Southern Ocean.
Most of the data from this project are available from the Marine Geoscience Data System (MGDS), part of IEDA and is available at https://www.marine-geo.org/tools/search/Files.php?data_set_uid=18148.";
String projects_0_end_date "2014-05";
String projects_0_geolocation "Southern Ocean";
String projects_0_name "Population ecology of Salpa thompsoni based on molecular indicators";
String projects_0_project_nid "2174";
String projects_0_start_date "2011-06";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing -66.183;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary
"This dataset is a log of the Salpa thompsoni specimens used for
genomics/transcriptomics. Reported parameters include cruise id, region,
season and area, location, number of samples collected, temperature, salinity,
depth range of the samples, and the depth of the water at the collection site.
Related Dataset: [Salp genome and transcriptome](\\\\https://www.bco-
dmo.org/dataset/675040\\\\)";
String title "[Salp sample log] - Salp specimen log for genomic and transcriptomic study collected from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project) (Population ecology of Salpa thompsoni based on molecular indicators)";
String version "1";
Float64 Westernmost_Easting -74.567;
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.