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Dataset Title:  Coral gene expression Sequence Read Archive (SRA) accession numbers and
information for samples collected at the Flower Garden Banks National Marine
Sanctuary in the Gulf of Mexico in September and October of 2017 to capture
effects of Hurricane Harvey
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_817298)
Range: longitude = -93.81469 to -93.60019°E, latitude = 27.8752 to 27.908°N, depth = 19.2 to 24.1m
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
 
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Things You Can Do With Your Graphs

Well, you can do anything you want with your graphs, of course. But some things you might not have considered are:

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Sample_Name {
    String bcodmo_name "sample";
    String description "Sample name";
    String long_name "Sample Name";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  }
  time2 {
    String bcodmo_name "Date_Month";
    String description "Sample time in format (Full month name and four digit year)";
    String long_name "Time";
    String units "unitless";
  }
  Bank {
    String bcodmo_name "site_descrip";
    String description "east or west bank of the  Flower Garden Banks";
    String long_name "Bank";
    String units "unitless";
  }
  Buoy {
    Float32 _FillValue NaN;
    Float32 actual_range 1.0, 4.0;
    String bcodmo_name "site_descrip";
    String description "Buoy number samples were collected from";
    String long_name "Buoy";
    String units "unitless";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float64 _FillValue NaN;
    Float64 actual_range 27.8752, 27.908;
    String axis "Y";
    String bcodmo_name "latitude";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "Sample latitude";
    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 -93.81469, -93.60019;
    String axis "X";
    String bcodmo_name "longitude";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "Sample longitude";
    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";
  }
  Species {
    String bcodmo_name "taxon";
    String description "Scientific name (Genus species)";
    String long_name "Species";
    String units "unitless";
  }
  depth {
    String _CoordinateAxisType "Height";
    String _CoordinateZisPositive "down";
    Float64 _FillValue NaN;
    Float64 actual_range 19.2, 24.1;
    String axis "Z";
    String bcodmo_name "depth";
    Float64 colorBarMaximum 8000.0;
    Float64 colorBarMinimum -8000.0;
    String colorBarPalette "TopographyDepth";
    String description "Sample 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";
  }
  SRA {
    String bcodmo_name "accession number";
    String description "Sequence Read Archive (SRA) accession number at NCBI";
    String long_name "SRA";
    String units "unitless";
  }
  Accession {
    String bcodmo_name "accession number";
    String description "BioSample accession number at NCBI";
    String long_name "Accession";
    String units "unitless";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
    String acquisition_description 
"Location:\\u00a0
 
East and west banks of the Flower Garden Banks National Marine Sanctuary
(FGBNMS) 80ft
 
Sampling Events:  
 Hurricane Harvey FGB October 2017, Hurricane Harvey FGB October 2018.
 
Methodology:\\u00a0
 
Tagseq libraries were prepared and SE 50bp reads were generated using Illumina
Hiseq 2500 platform.\\u00a0
 
Coral tissue samples were preserved midday underwater. RNA was isolated and
samples were processed for tagseq profiling.\\u00a0";
    String awards_0_award_nid "746827";
    String awards_0_award_number "OCE-1800904";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1800904";
    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 "Daniel Thornhill";
    String awards_0_program_manager_nid "722161";
    String cdm_data_type "Other";
    String comment 
"Hurricane Harvey sra samples 
  PI: Sarah Davies 
  Data Version 1: 2020-06-30";
    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 "2020-06-30T18:56:47Z";
    String date_modified "2020-07-08T14:50:47Z";
    String defaultDataQuery "&time<now";
    String doi "10.26008/1912/bco-dmo.817298.1";
    Float64 Easternmost_Easting -93.60019;
    Float64 geospatial_lat_max 27.908;
    Float64 geospatial_lat_min 27.8752;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -93.60019;
    Float64 geospatial_lon_min -93.81469;
    String geospatial_lon_units "degrees_east";
    Float64 geospatial_vertical_max 24.1;
    Float64 geospatial_vertical_min 19.2;
    String geospatial_vertical_positive "down";
    String geospatial_vertical_units "m";
    String history 
"2021-10-18T16:17:35Z (local files)
2021-10-18T16:17:35Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_817298.das";
    String infoUrl "https://www.bco-dmo.org/dataset/817298";
    String institution "BCO-DMO";
    String instruments_0_acronym "Automated Sequencer";
    String instruments_0_dataset_instrument_nid "817435";
    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 Hiseq 2500 platform";
    String keywords "accession, bank, bco, bco-dmo, biological, buoy, chemical, data, dataset, depth, dmo, erddap, latitude, longitude, management, name, oceanography, office, preliminary, sample, Sample_Name, species, sra, time, time2";
    String license "https://www.bco-dmo.org/dataset/817298/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/817298";
    Float64 Northernmost_Northing 27.908;
    String param_mapping "{'817298': {'Lat': 'master - latitude', 'Depth': 'master - depth', 'Lon': 'master - longitude'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/817298/parameters";
    String people_0_affiliation "Boston University";
    String people_0_affiliation_acronym "BU";
    String people_0_person_name "Sarah W. Davies";
    String people_0_person_nid "746829";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Boston University";
    String people_1_affiliation_acronym "BU";
    String people_1_person_name "Rachel Wright";
    String people_1_person_nid "817433";
    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 D. York";
    String people_2_person_nid "643627";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "Rapid Reefs Harvey";
    String projects_0_acronym "Rapid Reefs Harvey";
    String projects_0_description 
"NSF Award Abstract:
Coral reefs are ecologically and economically important ecosystems, and are threatened by a variety of global (climate change) and local (overfishing, pollution) stressors. Anthropogenic climate change is increasing the frequency and severity of storms, which can physically damage reef structures and reduce reef health through changes in seawater quality. In August of 2017, Hurricane Harvey caused widespread flooding in southeast Texas when it released more than 50 trillion liters of rain, which then accumulated along the Texas Shelf. This runoff is expected to impact nearby coral reefs in the Flower Garden Banks National Marine Sanctuary (FGBNMS, northwest Gulf of Mexico) via eddies and jets that transport coastal waters offshore. Findings from this project will allow managers to quickly predict whether extreme storm events are likely to induce reef mortality and ecosystem decline due to freshwater accumulation, by tracking of low salinity water masses coupled with microbial community characterization and metrics of coral health. These data are critical to managing coastal ecosystems, including the high coral cover reefs in the FGBNMS, and will help stakeholders (e.g., diving and fishing communities) plan for and minimize disruption to their livelihoods following these storms. Results will be communicated broadly across scientific arenas, in graduate and undergraduate education and training programs, and to the general public through outreach. The investigators have seven 7 square meter 2-D Reef Replicas from 2014 depicting representative FGBNMS reef bottoms, and will construct additional 2-D Reef Replicas from both banks following the arrival of Harvey runoff, allowing the public to directly experience and quantify the effects of Hurricane Harvey on local reefs using quadrats and identification guides. This project will also synergize with NSF REU programs at Boston University and Texas A&M University, providing transformative research experiences for undergraduates. One post-doctoral scholar, four graduate students, a technician and more than 5 undergraduates will be involved in all aspects of the research. All datasets will be made freely available to the public, and will serve as an important set of baselines for future lines of inquiry into the processes by which hurricanes and other extreme storms impact reef health.
Hurricanes and other extreme storm events can decimate coral reefs through wave-driven physical damage. Freshwater runoff from extreme storms is also potentially detrimental to reefs but has received comparatively less attention. This research will provide unprecedented resolution on how hurricanes and other extreme storm events may trigger cascading interactions among water chemistry, declines in metazoan health and shifts in their associated microbial communities, ultimately resulting in coral reef decline. The freshwater runoff initiated by Hurricane Harvey is likely to impact reefs within the FGBNMS, one of the few remaining coral-dominated reefs in the greater Caribbean. The effects of Harvey runoff will be compared to a previously documented storm-driven runoff event that was associated with invertebrate mortality on the same reef system. Sampling seawater chemistry, microbial communities (water column and benthic), and host gene expression and proteomics before, immediately after, and six months after Harvey runoff enters the FGBNMS will allow us to identify commonalities among large-scale freshwater runoff events and track the response of benthic invertebrate health, microbial community diversity, and the trajectory of reef community recovery or decline. The investigators will determine if changes in water chemistry induce pelagic microbial shifts, if microbial communities typically associated with corals and sponges are altered, and whether feedbacks occur between these potential drivers of benthic invertebrate mortality.";
    String projects_0_end_date "2019-11";
    String projects_0_geolocation "Flower Garden Banks National Marine Sanctuary, Northwest Gulf of Mexico";
    String projects_0_name "RAPID: Collaborative Research: Impact of freshwater runoff from Hurricane Harvey on coral reef benthic organisms and associated microbial communities";
    String projects_0_project_nid "746814";
    String projects_0_start_date "2017-12";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 27.8752;
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "To capture the immediate effects of storm-driven freshwater runoff on coral and symbiont physiology, we leveraged the heavy rainfall associated with Hurricane Harvey in late August 2017 by sampling FGB coral gene expression at two time points: September 2017, when surface water salinity was reduced (\\u223c34 ppt); and 1 month later when salinity had returned to typical levels (\\u223c36 ppt in October 2017). \\r\\n\\r\\nThis dataset includes Sequence Read Archive (SRA) and BioSample accessions under BioProject PRJNA552981 at The National Center for Biotechnology Information.  It also contains sample information and species names for samples collected the east and west banks of the Flower Garden Banks National Marine Sanctuary (FGBNMS) at 80ft.\\r\\n\\r\\nThese data were published in Wright et al. (2019).";
    String title "Coral gene expression Sequence Read Archive (SRA) accession numbers and information for samples collected at the Flower Garden Banks National Marine Sanctuary in the Gulf of Mexico in September and October of 2017 to capture effects of Hurricane Harvey";
    String version "1";
    Float64 Westernmost_Easting -93.81469;
    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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