ERDDAP > tabledap > Data Access Form

Dataset Title:	[FGB22 PSTR Coral Disease Microscopy & Omics] - Light microscopy images, Symbiodiniaceae electron micrographs, and NCBI Sequence Read Archive (SRA) accession numbers associated with diseased and healthy Pseudodiploria strigosa corals collected from the Flower Garden Banks National Marine Sanctuary (Collaborative Research: RAPID: A multi-scale approach to predicting coral disease spread: leveraging an outbreak on coral-dense isolated reefs)
Institution:	BCO-DMO   (Dataset ID: bcodmo_dataset_1010240_v1)
Information:	Summary | License | FGDC | ISO 19115 | Metadata | Background | Files | Make a graph

 

Variable	Optional Constraint #1		Optional Constraint #2		Minimum	Maximum
sample_id (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"001_DD"	"010_HH"
coral_id (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		1	10
col_health (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"diseased"	"healthy"
coral_species (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Pseudodiploria str..."	"Pseudodiploria str..."
coral_aphiaID (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		718718.0	718718.0
collection_date (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"2022-09-20"	"2022-09-21"
site (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"East Bank"	"West Bank"
buoy (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		2.0	5.0
depth_f (Depth_ft, feet)	!= =~ <= >= = < >		!= =~ <= >= = < >		61.0	79.0
latitude (degrees_north)	!= =~ <= >= = < >		!= =~ <= >= = < >		27.87532	27.9086
longitude (degrees_east)	!= =~ <= >= = < >		!= =~ <= >= = < >		-93.81482	-93.59718
ncbi_bioproject (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"PRJNA1292163"	"PRJNA1292163"
ncbi_biosample (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SAMN49992370"	"SAMN60298440"
ncbi_16S_sra (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SRX29707588"	"SRX29707600"
ncbi_ITS2_sra (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SRR38840713"	"SRR38840727"
ncbi_RNAseq_sra (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SRR39332190"	"SRR39332204"
TEM_file (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"001_DD_TEM.pdf"	"010_HH_TEM.pdf"
histo_file (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"001_DD_histo.pdf"	"010_HH_histo.pdf"

 

Server-side Functions

distinct()

orderBy orderByDescending orderByClosest orderByCount orderByLimit orderByMax orderByMin orderByMinMax orderByMean orderBySum (" sample_id coral_id col_health coral_species coral_aphiaID collection_date site buoy depth_f latitude longitude ncbi_bioproject ncbi_biosample ncbi_16S_sra ncbi_ITS2_sra ncbi_RNAseq_sra TEM_file histo_file sample_id coral_id col_health coral_species coral_aphiaID collection_date site buoy depth_f latitude longitude ncbi_bioproject ncbi_biosample ncbi_16S_sra ncbi_ITS2_sra ncbi_RNAseq_sra TEM_file histo_file sample_id coral_id col_health coral_species coral_aphiaID collection_date site buoy depth_f latitude longitude ncbi_bioproject ncbi_biosample ncbi_16S_sra ncbi_ITS2_sra ncbi_RNAseq_sra TEM_file histo_file sample_id coral_id col_health coral_species coral_aphiaID collection_date site buoy depth_f latitude longitude ncbi_bioproject ncbi_biosample ncbi_16S_sra ncbi_ITS2_sra ncbi_RNAseq_sra TEM_file histo_file sample_id coral_id col_health coral_species coral_aphiaID collection_date site buoy depth_f latitude longitude ncbi_bioproject ncbi_biosample ncbi_16S_sra ncbi_ITS2_sra ncbi_RNAseq_sra TEM_file histo_file ")

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_id {
    String long_name "Sample_id";
    String units "unitless";
  }
  coral_id {
    Int32 actual_range 1, 10;
    String long_name "Coral_id";
    String units "unitless";
  }
  col_health {
    String long_name "Col_health";
    String units "unitless";
  }
  coral_species {
    String long_name "Coral_species";
    String units "unitless";
  }
  coral_aphiaID {
    Float32 actual_range 718718.0, 718718.0;
    String long_name "Coral_aphiaid";
    String units "unitless";
  }
  collection_date {
    String long_name "Collection_date";
    String units "unitless";
  }
  site {
    String long_name "Site";
    String units "unitless";
  }
  buoy {
    Float32 actual_range 2.0, 5.0;
    String long_name "Buoy";
    String units "unitless";
  }
  depth_f {
    Float32 actual_range 61.0, 79.0;
    String long_name "Depth_ft";
    String units "feet";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float32 actual_range 27.87532, 27.9086;
    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 -93.81482, -93.59718;
    String axis "X";
    String ioos_category "Location";
    String long_name "Longitude";
    String standard_name "longitude";
    String units "degrees_east";
  }
  ncbi_bioproject {
    String long_name "Ncbi_bioproject";
    String units "unitless";
  }
  ncbi_biosample {
    String long_name "Ncbi_biosample";
    String units "unitless";
  }
  ncbi_16S_sra {
    String long_name "Ncbi_16s_sra";
    String units "unitless";
  }
  ncbi_ITS2_sra {
    String long_name "Ncbi_its2_sra";
    String units "unitless";
  }
  ncbi_RNAseq_sra {
    String long_name "Ncbi_rnaseq_sra";
    String units "unitless";
  }
  TEM_file {
    String long_name "Tem_file";
    String units "unitless";
  }
  histo_file {
    String long_name "Histo_file";
    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.1010240.1";
    Float64 Easternmost_Easting -93.59718;
    Float64 geospatial_lat_max 27.9086;
    Float64 geospatial_lat_min 27.87532;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -93.59718;
    Float64 geospatial_lon_min -93.81482;
    String geospatial_lon_units "degrees_east";
    String history 
"2026-10-30T16:16:41Z (local files)
2026-10-30T16:16:41Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_1010240_v1.html";
    String infoUrl "https://osprey.bco-dmo.org/dataset/1010240";
    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 27.9086;
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 27.87532;
    String summary "This dataset includes microscopy and omics data associated with 15 apparently healthy and diseased Pseudodiploria strigosa corals collected from the Flower Garden Banks National Marine Sanctuary (Northwest Gulf of Mexico) in September 2022, one month after a coral disease outbreak. Samples were collected from pairs of apparently healthy corals (HH tissue; n=5) and diseased corals (n=5). From diseased corals, two tissue samples were taken: apparently healthy tissue (HD) and disease-adjacent tissue (DD). Histopathology light microscopy images and electron micrographs of Symbiodiniaceae cells generated with transmission electron microscopy (TEM) are included as PDF files sorted by sample. These data also include NCBI Sequence Read Archive (SRA) accession numbers for raw fastq files of 16S rRNA gene sequencing, internal transcribed spacer-2 (ITS-2) sequencing, and RNA-Seq. This dataset supports an integrative approach for characterizing signatures of marine diseases at cellular, sub-cellular, and gene expression levels spanning multiple holobiont members: the coral host, Symbiodiniaceae microeukaryotes, bacteria/archaea communities, and viruses.";
    String title "[FGB22 PSTR Coral Disease Microscopy & Omics] - Light microscopy images, Symbiodiniaceae electron micrographs, and NCBI Sequence Read Archive (SRA) accession numbers associated with diseased and healthy Pseudodiploria strigosa corals collected from the Flower Garden Banks National Marine Sanctuary (Collaborative Research: RAPID: A multi-scale approach to predicting coral disease spread: leveraging an outbreak on coral-dense isolated reefs)";
    Float64 Westernmost_Easting -93.81482;
  }
}

 

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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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