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Dataset Title:	[SCTLD-associated Symbiodiniaceae ITS-2] - NCBI Sequence Read Archive (SRA) accession numbers for raw fastq sequence files of ITS-2 amplicons collected from healthy and SCTLD-affected tissues of nine coral species in Florida, U.S. A. and the U.S. Virgin Islands from 2018-2020 (A multi-scale approach to predicting infectious multi-host disease spread in marine benthic communities)
Institution:	BCO-DMO   (Dataset ID: bcodmo_dataset_997771_v1)
Information:	Summary | License | FGDC | ISO 19115 | Metadata | Background | Files | Make a graph

 

Variable	Optional Constraint #1		Optional Constraint #2		Minimum	Maximum
sample (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"C10_S73"	"p64_S181"
coral_id (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"CNAT_1"	"SSID_327"
sample_id (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"CNAT_1345a-c1-tf"	"SSID_327D_S2"
health (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"diseased"	"unaffected"
host_phylum (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Cnidaria"	"Cnidaria"
host_class (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Anthozoa"	"Hexacorallia"
host_order (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Scleractinia"	"Scleractinia"
host_family (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Faviidae"	"Siderastreidae"
host_genus (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Colpophyllia"	"Siderastrea"
host_species (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"annularis"	"strigosa"
susceptibility (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"high"	"moderate"
location (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"FL"	"USVI"
sampletype (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"experiment_t1"	"field_hh"
site (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Black_Point"	"West_Turtle_Shoal"
latitude (degrees_north)	!= =~ <= >= = < >		!= =~ <= >= = < >		18.27925	24.7329
longitude (degrees_east)	!= =~ <= >= = < >		!= =~ <= >= = < >		-81.4095	-64.89533
year (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"2018"	"2020"
col_health (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"diseased"	"healthy"
figure_sample_id (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"CNAT_DD_25"	"SSID_HH_9_Tf"
figure_coral_id (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"CNAT_1"	"SSID_9"
ncbi_bioproject (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"PRJNA1230223"	"PRJNA955224"
ncbi_biosample (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SAMN35677892"	"SAMN53696825"
AphiaID (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		207516	758261

 

Server-side Functions

distinct()

orderBy orderByDescending orderByClosest orderByCount orderByLimit orderByMax orderByMin orderByMinMax orderByMean orderBySum (" sample coral_id sample_id health host_phylum host_class host_order host_family host_genus host_species susceptibility location sampletype site latitude longitude year col_health figure_sample_id figure_coral_id ncbi_bioproject ncbi_biosample AphiaID sample coral_id sample_id health host_phylum host_class host_order host_family host_genus host_species susceptibility location sampletype site latitude longitude year col_health figure_sample_id figure_coral_id ncbi_bioproject ncbi_biosample AphiaID sample coral_id sample_id health host_phylum host_class host_order host_family host_genus host_species susceptibility location sampletype site latitude longitude year col_health figure_sample_id figure_coral_id ncbi_bioproject ncbi_biosample AphiaID sample coral_id sample_id health host_phylum host_class host_order host_family host_genus host_species susceptibility location sampletype site latitude longitude year col_health figure_sample_id figure_coral_id ncbi_bioproject ncbi_biosample AphiaID sample coral_id sample_id health host_phylum host_class host_order host_family host_genus host_species susceptibility location sampletype site latitude longitude year col_health figure_sample_id figure_coral_id ncbi_bioproject ncbi_biosample AphiaID ")

File type: (more information) .asc - View OPeNDAP-style ISO-8859-1 comma-separated text. .csv - Download a ISO-8859-1 comma-separated text table (line 1: names; line 2: units; ISO 8601 times). .csvp - Download a ISO-8859-1 .csv file with line 1: name (units). Times are ISO 8601 strings. .csv0 - Download a ISO-8859-1 .csv file without column names or units. Times are ISO 8601 strings. .dataTable - A JSON file formatted for use with the Google Visualization client library (Google Charts). .das - View the dataset's metadata via an ISO-8859-1 OPeNDAP Dataset Attribute Structure (DAS). .dds - View the dataset's structure via an ISO-8859-1 OPeNDAP Dataset Descriptor Structure (DDS). .dods - OPeNDAP clients use this to download the data in the DODS binary format. .esriCsv - Download a ISO_8859_1 .csv file for ESRI's ArcGIS 9.x and below (separate date and time columns). .fgdc - View the dataset's UTF-8 FGDC .xml metadata. .geoJson - Download longitude,latitude,otherColumns data as a UTF-8 GeoJSON .json file. .graph - View a Make A Graph web page. .help - View a web page with a description of tabledap. .html - View an OPeNDAP-style HTML Data Access Form. .htmlTable - View a UTF-8 .html web page with the data in a table. Times are ISO 8601 strings. .iso19115 - View the dataset's ISO 19115-2/19139 UTF-8 .xml metadata. .itx - Download an ISO-8859-1 Igor Text File. Each response column becomes a wave. .json - View a table-like UTF-8 JSON file (missing value = 'null'; times are ISO 8601 strings). .jsonlCSV1 - View a UTF-8 JSON Lines CSV file with column names on line 1 (mv = 'null'; times are ISO 8601 strings). .jsonlCSV - View a UTF-8 JSON Lines CSV file without column names (mv = 'null'; times are ISO 8601 strings). .jsonlKVP - View a UTF-8 JSON Lines file with Key:Value pairs (missing value = 'null'; times are ISO 8601 strings). .mat - Download a MATLAB binary file. .nc - Download a flat, table-like, NetCDF-3 binary file with COARDS/CF/ACDD metadata. .ncHeader - View the UTF-8 header (the metadata) for the NetCDF-3 .nc file. .ncCF - Download a NetCDF-3 CF Discrete Sampling Geometries file (Contiguous Ragged Array). .ncCFHeader - View the UTF-8 header (the metadata) for the .ncCF file. .ncCFMA - Download a NetCDF-3 CF Discrete Sampling Geometries file (Multidimensional Array). .ncCFMAHeader - View the UTF-8 header (the metadata) for the .ncCFMA file. .nccsv - Download a NetCDF-3-like 7-bit ASCII NCCSV .csv file with COARDS/CF/ACDD metadata. .nccsvMetadata - View the dataset's metadata as the top half of a 7-bit ASCII NCCSV .csv file. .ncoJson - Download a UTF-8 NCO lvl=2 JSON file with COARDS/CF/ACDD metadata. .odvTxt - Download longitude,latitude,time,otherColumns as an ISO-8859-1 ODV Generic Spreadsheet File (.txt). .subset - View an HTML form which uses faceted search to simplify picking subsets of the data. .tsv - Download a ISO-8859-1 tab-separated text table (line 1: names; line 2: units; ISO 8601 times). .tsvp - Download a ISO-8859-1 .tsv file with line 1: name (units). Times are ISO 8601 strings. .tsv0 - Download a ISO-8859-1 .tsv file without column names or units. Times are ISO 8601 strings. .wav - Download a .wav audio file. All columns must be numeric and of the same type. .xhtml - View a UTF-8 XHTML (XML) file with the data in a table. Times are ISO 8601 strings. .kml - View a .kml file, suitable for Google Earth. .smallPdf - View a small .pdf image file with a graph or map. .pdf - View a standard, medium-sized .pdf image file with a graph or map. .largePdf - View a large .pdf image file with a graph or map. .smallPng - View a small .png image file with a graph or map. .png - View a standard, medium-sized .png image file with a graph or map. .largePng - View a large .png image file with a graph or map. .transparentPng - View a .png image file (just the data, without axes, landmask, or legend).

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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  sample {
    String long_name "Sample";
    String units "unitless";
  }
  coral_id {
    String long_name "Coral_id";
    String units "unitless";
  }
  sample_id {
    String long_name "Sample_id";
    String units "unitless";
  }
  health {
    String long_name "Health";
    String units "unitless";
  }
  host_phylum {
    String long_name "Host_phylum";
    String units "unitless";
  }
  host_class {
    String long_name "Host_class";
    String units "unitless";
  }
  host_order {
    String long_name "Host_order";
    String units "unitless";
  }
  host_family {
    String long_name "Host_family";
    String units "unitless";
  }
  host_genus {
    String long_name "Host_genus";
    String units "unitless";
  }
  host_species {
    String long_name "Host_species";
    String units "unitless";
  }
  susceptibility {
    String long_name "Susceptibility";
    String units "unitless";
  }
  location {
    String long_name "Location";
    String units "unitless";
  }
  sampletype {
    String long_name "Sampletype";
    String units "unitless";
  }
  site {
    String long_name "Site";
    String units "unitless";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float32 actual_range 18.27925, 24.7329;
    String axis "Y";
    String ioos_category "Location";
    String long_name "Latitude";
    String standard_name "latitude";
    String units "degrees_north";
  }
  longitude {
    String _CoordinateAxisType "Lon";
    Float32 actual_range -81.4095, -64.89533;
    String axis "X";
    String ioos_category "Location";
    String long_name "Longitude";
    String standard_name "longitude";
    String units "degrees_east";
  }
  year {
    String long_name "Year";
    String units "unitless";
  }
  col_health {
    String long_name "Col_health";
    String units "unitless";
  }
  figure_sample_id {
    String long_name "Figure_sample_id";
    String units "unitless";
  }
  figure_coral_id {
    String long_name "Figure_coral_id";
    String units "unitless";
  }
  ncbi_bioproject {
    String long_name "Ncbi_bioproject";
    String units "unitless";
  }
  ncbi_biosample {
    String long_name "Ncbi_biosample";
    String units "unitless";
  }
  AphiaID {
    Int32 actual_range 207516, 758261;
    String long_name "Aphiaid";
    String units "unitless";
  }
 }
  NC_GLOBAL {
    String cdm_data_type "Other";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_url "https://www.bco-dmo.org/";
    String doi "10.26008/1912/bco-dmo.997771.1";
    Float64 Easternmost_Easting -64.89533;
    Float64 geospatial_lat_max 24.7329;
    Float64 geospatial_lat_min 18.27925;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -64.89533;
    Float64 geospatial_lon_min -81.4095;
    String geospatial_lon_units "degrees_east";
    String history 
"2026-05-15T21:35:45Z (local files)
2026-05-15T21:35:45Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_997771_v1.html";
    String infoUrl "https://osprey.bco-dmo.org/dataset/997771";
    String institution "BCO-DMO";
    String license 
"The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.";
    Float64 Northernmost_Northing 24.7329;
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 18.27925;
    String summary "These data include NCBI Sequence Read Archive (SRA) accession numbers for raw fastq files of internal transcribed spacer-2 (ITS-2) amplicons from 491 apparently healthy and stony coral tissue loss disease (SCTLD)-affected corals in Florida, U.S.A., and the United States Virgin Islands (USVI), representing nine coral species sampled in situ or during an SCTLD transmission experiment. From Florida, 215 samples were collected in situ from six epidemic sites in 2018. From the USVI, 110 samples were collected in situ from four reef sites in 2019-2020. Of the total samples, 325 were sampled in situ as sets of SCTLD-affected and apparently healthy conspecifics: two samples were collected from each diseased coral, one from tissue adjacent to the gross tissue loss lesion and one from apparently healthy tissue on the same coral; one sample was then collected from a nearby conspecific coral that was apparently healthy. The 166 remaining samples were originally collected from Rupert's Rock in the USVI, and samples were taken from these corals during a wet lab-based SCTLD transmission experiment. Understanding whether Symbiodiniaceae composition is predictive of disease state is crucial for managing SCTLD outbreaks, and these data permit investigations of how Symbiodiniaceae lineage-level dynamics may underlie variation in holobiont disease response. Florida samples were collected by Kerry Maxwell, Lindsay Huebner, Dr. Erinn M. Muller, and their teams at the Florida Fish & Wildlife Research Institute and Mote Marine Laboratory. USVI samples were collected by Dr. Marilyn Brandt, Sonora Meiling, Dr. Alex Veglia, Dr. Daniel Holstein, Dr. Laura Mydlarz, Dr. Amy Apprill, Dr. Adrienne Correa, and their teams. Danielle Lasseigne, Adam Glahn, Amanda Long, Bradley Arrington, Daniel Mele, Kathryn Cobleigh, Alexandra Gutting, Joseph Townsend, Naomi Huntley, Kelsey Beavers, Paul Barbera, Nate Berkebile, Tiffany Boisvert, Michael Bollinger, Katy Cummings, Amanda Ellis, Kristine Fisher, John Hart, Lauri Maclaughlin, Brian Reckenbeil, and Jennifer Stein assisted with field collections.";
    String title "[SCTLD-associated Symbiodiniaceae ITS-2] - NCBI Sequence Read Archive (SRA) accession numbers for raw fastq sequence files of ITS-2 amplicons collected from healthy and SCTLD-affected tissues of nine coral species in Florida, U.S.A. and the U.S. Virgin Islands from 2018-2020 (A multi-scale approach to predicting infectious multi-host disease spread in marine benthic communities)";
    Float64 Westernmost_Easting -81.4095;
  }
}

 

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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 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.

• (easy) You can get data by using the dataset's Data Access Form or Subset form. They make the URL for you.
• (easy) You can make a graph or map by using the dataset's Make A Graph form. It makes the URL for you.
• (not hard) You can bypass the forms and get the data or make a graph or map by generating the URL by hand or with a computer program or script.

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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