Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | [Metabarcoding zooplankton at station ALOHA: NCBI SRA accession numbers] - NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample (Plankton Population Genetics project) (Basin- scale genetics of marine zooplankton) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_700961) |
| Information: | Summary
| License
| FGDC
| ISO 19115
| Metadata
| Background
| Subset
| Files
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Attributes {
s {
analysis_name {
String bcodmo_name "sample_descrip";
String description "Descriptive name of analysis including percent clustering and subsampling or no subsampling";
String long_name "Analysis Name";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 22.75, 22.75;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude of sample site (Station ALOHA)";
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 -158.0, -158.0;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude of sample site (Station ALOHA)";
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";
}
library_ID {
String bcodmo_name "sample";
String description "Short unique identifier for the sequencing library.";
String long_name "Library ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
bioproject_accession {
String bcodmo_name "accession number";
String description "NCBI BioProject identifier";
String long_name "Bioproject Accession";
String units "unitless";
}
biosample_accession {
String bcodmo_name "accession number";
String description "NCBI BioSample identifier";
String long_name "Biosample Accession";
String units "unitless";
}
title {
String bcodmo_name "sample_descrip";
String description "Short description that will identify the dataset on public pages.";
String long_name "Title";
String units "unitless";
}
library_strategy {
String bcodmo_name "sample_descrip";
String description "Amplicon = Sequencing of overlapping or distinct PCR or RT-PCR products";
String long_name "Library Strategy";
String units "unitless";
}
library_source {
String bcodmo_name "sample_descrip";
String description "Metagenomic = Mixed material from metagenome";
String long_name "Library Source";
String units "unitless";
}
library_selection {
String bcodmo_name "sample_descrip";
String description "PCR = Source material was selected by designed primers";
String long_name "Library Selection";
String units "unitless";
}
library_layout {
String bcodmo_name "sample_descrip";
String description "Paired-end or Single";
String long_name "Library Layout";
String units "unitless";
}
platform {
String bcodmo_name "sample_descrip";
String description "Sequencing platforms [Illumina]";
String long_name "Platform";
String units "unitless";
}
instrument_model {
String bcodmo_name "instrument";
String description "Illumina instrument and model used for sequencing";
String long_name "Instrument Model";
String units "unitless";
}
design_description {
String bcodmo_name "sample_descrip";
String description "Free-form description of the methods used to create the sequencing library; a brief materials and methods section.";
String long_name "Design Description";
String units "unitless";
}
bioproject_link {
String bcodmo_name "unknown";
String description "bioproject_link";
String long_name "Bioproject Link";
String units "unitless";
}
biosample_link {
String bcodmo_name "unknown";
String description "biosample_link";
String long_name "Biosample Link";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"SAMPLE INFORMATION
Sample identifiers include the following codes.
MOCNESS tow
FA3: Night sampling
FA4: Day sampling
Depth range:
N1: 1500-1000m
N2: 1000-700m
N3: 700-500m
N4: 500-300m
N5: 300-200m
N6: 200-150m
N7: 150-100m
N8: 100-50m
N9: 50m-0m
Wet-sieved zooplankton size fractions
SF1: 0.2-0.5 mm
SF2: 0.5-1.0 mm
SF3: 1.0-2.0 mm";
String awards_0_award_nid "473046";
String awards_0_award_number "OCE-1255697";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1255697";
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 "537990";
String awards_1_award_number "OCE-1338959";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1338959";
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 awards_2_award_nid "539716";
String awards_2_award_number "OCE-1029478";
String awards_2_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1029478";
String awards_2_funder_name "NSF Division of Ocean Sciences";
String awards_2_funding_acronym "NSF OCE";
String awards_2_funding_source_nid "355";
String awards_2_program_manager "David L. Garrison";
String awards_2_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"ALOHA Zooplankton metabarcoding: SRA
PI: Erica Goetze
data version: 07 Jun 2017";
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 "2017-05-25T19:52:10Z";
String date_modified "2017-08-02T12:08:50Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.704665";
Float64 Easternmost_Easting -158.0;
Float64 geospatial_lat_max 22.75;
Float64 geospatial_lat_min 22.75;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -158.0;
Float64 geospatial_lon_min -158.0;
String geospatial_lon_units "degrees_east";
String history
"2024-11-21T11:26:41Z (local files)
2024-11-21T11:26:41Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_700961.html";
String infoUrl "https://www.bco-dmo.org/dataset/700961";
String institution "BCO-DMO";
String instruments_0_acronym "Automated Sequencer";
String instruments_0_dataset_instrument_description "Illumina MiSeq using V3 chemistry (300-bp, paired-end)";
String instruments_0_dataset_instrument_nid "700970";
String instruments_0_description "General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.";
String instruments_0_instrument_name "Automated DNA Sequencer";
String instruments_0_instrument_nid "649";
String instruments_0_supplied_name "Illumina MiSeq";
String instruments_1_acronym "Thermal Cycler";
String instruments_1_dataset_instrument_nid "700972";
String instruments_1_description
"General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)";
String instruments_1_instrument_name "PCR Thermal Cycler";
String instruments_1_instrument_nid "471582";
String instruments_1_supplied_name "quantitative PCR by the Evolutionary Genetics Core Facility (Hawaii Institute of Marine Biology)";
String instruments_2_acronym "Bioanalyzer";
String instruments_2_dataset_instrument_nid "700971";
String instruments_2_description "A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100.";
String instruments_2_instrument_name "Bioanalyzer";
String instruments_2_instrument_nid "626182";
String instruments_2_supplied_name "Agilent 2100 Bioanalyzer";
String keywords "accession, analysis, analysis_name, bco, bco-dmo, biological, bioproject, bioproject_accession, bioproject_link, biosample, biosample_accession, biosample_link, chemical, data, dataset, description, design, design_description, dmo, erddap, instrument, instrument_model, latitude, layout, library, library_ID, library_layout, library_selection, library_source, library_strategy, link, longitude, management, model, name, oceanography, office, platform, preliminary, selection, source, strategy, title";
String license "https://www.bco-dmo.org/dataset/700961/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/700961";
Float64 Northernmost_Northing 22.75;
String param_mapping "{'700961': {'lat': 'master - latitude', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/700961/parameters";
String people_0_affiliation "University of Hawaii";
String people_0_person_name "Erica Goetze";
String people_0_person_nid "473048";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of Hawaii";
String people_1_person_name "Erica Goetze";
String people_1_person_nid "473048";
String people_1_role "Contact";
String people_1_role_type "related";
String people_2_affiliation "Woods Hole Oceanographic Institution";
String people_2_affiliation_acronym "WHOI BCO-DMO";
String people_2_person_name "Amber York";
String people_2_person_nid "643627";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "Plankton Population Genetics";
String projects_0_acronym "Plankton Population Genetics";
String projects_0_description
"Description from NSF award abstract:
Marine zooplankton show strong ecological responses to climate change, but little is known about their capacity for evolutionary response. Many authors have assumed that the evolutionary potential of zooplankton is limited. However, recent studies provide circumstantial evidence for the idea that selection is a dominant evolutionary force acting on these species, and that genetic isolation can be achieved at regional spatial scales in pelagic habitats. This RAPID project will take advantage of a unique opportunity for basin-scale transect sampling through participation in the Atlantic Meridional Transect (AMT) cruise in 2014. The cruise will traverse more than 90 degrees of latitude in the Atlantic Ocean and include boreal-temperate, subtropical and tropical waters. Zooplankton samples will be collected along the transect, and mitochondrial and microsatellite markers will be used to identify the geographic location of strong genetic breaks within three copepod species. Bayesian and coalescent analytical techniques will test if these regions act as dispersal barriers. The physiological condition of animals collected in distinct ocean habitats will be assessed by measurements of egg production (at sea) as well as body size (condition index), dry weight, and carbon and nitrogen content. The PI will test the prediction that ocean regions that serve as dispersal barriers for marine holoplankton are areas of poor-quality habitat for the target species, and that this is a dominant mechanism driving population genetic structure in oceanic zooplankton.
Note: This project is funded by an NSF RAPID award. This RAPID grant supported the shiptime costs, and all the sampling reported in the AMT24 zooplankton ecology cruise report (PDF).
Online science outreach blog at: https://atlanticplankton.wordpress.com";
String projects_0_end_date "2015-11";
String projects_0_geolocation "Atlantic Ocean, 46 N - 46 S";
String projects_0_name "Basin-scale genetics of marine zooplankton";
String projects_0_project_nid "537991";
String projects_0_start_date "2013-12";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 22.75;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "latitude,longitude,bioproject_accession,title,library_strategy,library_source,library_selection,library_layout,platform,instrument_model,design_description,bioproject_link";
String summary
"These data include sample information and accession links to sequence data at
The National Center for Biotechnology Information (NCBI) Sequence Read Archive
(SRA).
This data submission consists of metabarcoding data for the zooplankton
community in the epipelagic, mesopelagic and upper bathypelagic zones
(0-1500m) of the North Pacific Subtropical Gyre. The goal of this study was to
assess the hidden diversity present in zooplankton assemblages in midwaters,
and detect vertical gradients in species richness, depth distributions, and
community composition of the full zooplankton assemblage. Samples were
collected in June 2014 from Station ALOHA (22.75, -158) using a 1 meter square
Multiple Opening and Closing Nets and Environmental Sampling System (MOCNESS,
200um mesh), on R/V Falkor cruise FK140613. \\u00a0Next generation sequence
data (Illumina MiSeq, V3 chemistry, 300-bp paired-end) of the zooplankton
assemblage derive from amplicons of the V1-V2 region of 18S rRNA (primers
described in Fonseca et al. 2010). The data includes sequences and read count
abundance information for molecular OTUs from both holoplanktonic and
meroplanktonic taxa
Related dataset containing OTU tables and fasta sequences (representative /
most abundance read for each OTU):
[Metabarcoding zooplankton at ](\\\\http://www.bco-
dmo.org/dataset/700279\\\\)[station](\\\\http://www.bco-
dmo.org/dataset/700279\\\\)[ ALOHA: OTU tables and ](\\\\http://www.bco-
dmo.org/dataset/700279\\\\)[fasta](\\\\http://www.bco-
dmo.org/dataset/700279\\\\)[ files](\\\\http://www.bco-
dmo.org/dataset/700279\\\\)";
String title "[Metabarcoding zooplankton at station ALOHA: NCBI SRA accession numbers] - NCBI Sequence Read Archive (SRA) accession numbers for fastq sequence files for each zooplankton community sample (Plankton Population Genetics project) (Basin-scale genetics of marine zooplankton)";
String version "1";
Float64 Westernmost_Easting -158.0;
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.