ERDDAP > tabledap > Data Access Form

Dataset Title:	[RECHARGE 2018 - 2020 Microbiome Data] - Sequence read accession (SRA) numbers and collection metadata for coral microbiome collected in Moorea, French Polynesia from Jul 2018 to Aug 2020 (Collaborative Research: Tipping points in coral reefs and their associated microbiomes: interactive effects of herbivory, nutrient enrichment, and temperature)
Institution:	BCO-DMO   (Dataset ID: bcodmo_dataset_954262_v1)
Information:	Summary | License | FGDC | ISO 19115 | Metadata | Background | Files | Make a graph

 

Variable	Optional Constraint #1		Optional Constraint #2		Minimum	Maximum
Sample (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"lane1-s001-index--..."	"lane1-s290-index-T..."
Date_MonthYear (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Aug19"	"Nov19"
Coral_Code (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Aret"	"control"
Herbivory (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"1x1"	"open"
Nutrients (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Ambient"	"multi"
Plot (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"A1"	"multi"
Tag (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"100"	"multi"
Batch (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"R1"	"R3"
Run (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SRR25266994"	"SRR25267752"
AssayType (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"AMPLICON"	"AMPLICON"
AvgSpotLen (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		602	602
Bases (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		6020	247114980
BioProject (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"PRJNA994532"	"PRJNA994532"
BioSample (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SAMN36436051"	"SAMN36436809"
BioSampleModel (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"MIGS/MIMS/MIMARKS...."	"MIMARKS.survey,MIG..."
Bytes (bytes)	!= =~ <= >= = < >		!= =~ <= >= = < >		65709	136616240
CenterName (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"OREGON STATE UNIVE..."	"OREGON STATE UNIVE..."
Collection_Date (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"2018-07"	"2021-05"
Consent (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"public"	"public"
DATASTORE_filetype (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"fastq,run.zq,sra"	"sra,fastq,run.zq"
DATASTORE_provider (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"gs,ncbi,s3"	"gs,ncbi,s3"
DATASTORE_region (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"gs.us-east1,ncbi.p..."	"gs.us-east1,ncbi.p..."
env_broad_scale (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Research Laboratory"	"Tropical South Pac..."
env_local_scale (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"North shore fore r..."	"Reagent control"
env_medium (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Algal Tissue"	"PCR water"
Experiment (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SRX21012823"	"SRX21013581"
geo_loc_name_country (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"French Polynesia"	"USA"
geo_loc_name_country_continent (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"North America"	"Oceania"
geo_loc_name (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"French Polynesia: ..."	"USA: Oregon State ..."
Host (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Acropora retusa"	"not applicable"
Instrument (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Illumina MiSeq"	"Illumina MiSeq"
latitude (degrees_north)	!= =~ <= >= = < >		!= =~ <= >= = < >		-17.4731	44.56631
longitude (degrees_east)	!= =~ <= >= = < >		!= =~ <= >= = < >		-149.8177	-123.2829
LibraryName (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"lane1-s001-index--..."	"lane1-s290-index-T..."
LibraryLayout (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"PAIRED"	"PAIRED"
LibrarySelection (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"PCR"	"PCR"
LibrarySource (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"METAGENOMIC"	"METAGENOMIC"
Organism (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"algae metagenome"	"indoor metagenome"
Platform (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"ILLUMINA"	"ILLUMINA"
ReleaseDate (UTC)	!= =~ <= >= = < >		!= =~ <= >= = < >
create_date (UTC)	!= =~ <= >= = < >		!= =~ <= >= = < >
version (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		1	1
SRA_Study (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SRP449431"	"SRP449431"
unique_sample_identifier (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		1	759

 

Server-side Functions

distinct()

orderBy orderByDescending orderByClosest orderByCount orderByLimit orderByMax orderByMin orderByMinMax orderByMean orderBySum (" Sample Date_MonthYear Coral_Code Herbivory Nutrients Plot Tag Batch Run AssayType AvgSpotLen Bases BioProject BioSample BioSampleModel Bytes CenterName Collection_Date Consent DATASTORE_filetype DATASTORE_provider DATASTORE_region env_broad_scale env_local_scale env_medium Experiment geo_loc_name_country geo_loc_name_country_continent geo_loc_name Host Instrument latitude longitude LibraryName LibraryLayout LibrarySelection LibrarySource Organism Platform ReleaseDate create_date version SRA_Study unique_sample_identifier Sample Date_MonthYear Coral_Code Herbivory Nutrients Plot Tag Batch Run AssayType AvgSpotLen Bases BioProject BioSample BioSampleModel Bytes CenterName Collection_Date Consent DATASTORE_filetype DATASTORE_provider DATASTORE_region env_broad_scale env_local_scale env_medium Experiment geo_loc_name_country geo_loc_name_country_continent geo_loc_name Host Instrument latitude longitude LibraryName LibraryLayout LibrarySelection LibrarySource Organism Platform ReleaseDate create_date version SRA_Study unique_sample_identifier Sample Date_MonthYear Coral_Code Herbivory Nutrients Plot Tag Batch Run AssayType AvgSpotLen Bases BioProject BioSample BioSampleModel Bytes CenterName Collection_Date Consent DATASTORE_filetype DATASTORE_provider DATASTORE_region env_broad_scale env_local_scale env_medium Experiment geo_loc_name_country geo_loc_name_country_continent geo_loc_name Host Instrument latitude longitude LibraryName LibraryLayout LibrarySelection LibrarySource Organism Platform ReleaseDate create_date version SRA_Study unique_sample_identifier Sample Date_MonthYear Coral_Code Herbivory Nutrients Plot Tag Batch Run AssayType AvgSpotLen Bases BioProject BioSample BioSampleModel Bytes CenterName Collection_Date Consent DATASTORE_filetype DATASTORE_provider DATASTORE_region env_broad_scale env_local_scale env_medium Experiment geo_loc_name_country geo_loc_name_country_continent geo_loc_name Host Instrument latitude longitude LibraryName LibraryLayout LibrarySelection LibrarySource Organism Platform ReleaseDate create_date version SRA_Study unique_sample_identifier Sample Date_MonthYear Coral_Code Herbivory Nutrients Plot Tag Batch Run AssayType AvgSpotLen Bases BioProject BioSample BioSampleModel Bytes CenterName Collection_Date Consent DATASTORE_filetype DATASTORE_provider DATASTORE_region env_broad_scale env_local_scale env_medium Experiment geo_loc_name_country geo_loc_name_country_continent geo_loc_name Host Instrument latitude longitude LibraryName LibraryLayout LibrarySelection LibrarySource Organism Platform ReleaseDate create_date version SRA_Study unique_sample_identifier ")

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";
  }
  Date_MonthYear {
    String long_name "Date_monthyear";
    String units "unitless";
  }
  Coral_Code {
    String long_name "Coral_code";
    String units "unitless";
  }
  Herbivory {
    String long_name "Herbivory";
    String units "unitless";
  }
  Nutrients {
    String long_name "Nutrients";
    String units "unitless";
  }
  Plot {
    String long_name "Plot";
    String units "unitless";
  }
  Tag {
    String long_name "Tag";
    String units "unitless";
  }
  Batch {
    String long_name "Batch";
    String units "unitless";
  }
  Run {
    String long_name "Run";
    String units "unitless";
  }
  AssayType {
    String long_name "Assaytype";
    String units "unitless";
  }
  AvgSpotLen {
    Int32 actual_range 602, 602;
    String long_name "Avgspotlen";
    String units "unitless";
  }
  Bases {
    Int32 actual_range 6020, 247114980;
    String long_name "Bases";
    String units "unitless";
  }
  BioProject {
    String long_name "Bioproject";
    String units "unitless";
  }
  BioSample {
    String long_name "Biosample";
    String units "unitless";
  }
  BioSampleModel {
    String long_name "Biosamplemodel";
    String units "unitless";
  }
  Bytes {
    Int32 actual_range 65709, 136616240;
    String long_name "Bytes";
    String units "bytes";
  }
  CenterName {
    String long_name "Centername";
    String units "unitless";
  }
  Collection_Date {
    String long_name "Collection_date";
    String units "unitless";
  }
  Consent {
    String long_name "Consent";
    String units "unitless";
  }
  DATASTORE_filetype {
    String long_name "Datastore_filetype";
    String units "unitless";
  }
  DATASTORE_provider {
    String long_name "Datastore_provider";
    String units "unitless";
  }
  DATASTORE_region {
    String long_name "Datastore_region";
    String units "unitless";
  }
  env_broad_scale {
    String long_name "Env_broad_scale";
    String units "unitless";
  }
  env_local_scale {
    String long_name "Env_local_scale";
    String units "unitless";
  }
  env_medium {
    String long_name "Env_medium";
    String units "unitless";
  }
  Experiment {
    String long_name "Experiment";
    String units "unitless";
  }
  geo_loc_name_country {
    String long_name "Geo_loc_name_country";
    String units "unitless";
  }
  geo_loc_name_country_continent {
    String long_name "Geo_loc_name_country_continent";
    String units "unitless";
  }
  geo_loc_name {
    String long_name "Geo_loc_name";
    String units "unitless";
  }
  Host {
    String long_name "Host";
    String units "unitless";
  }
  Instrument {
    String long_name "Instrument";
    String units "unitless";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float32 actual_range -17.4731, 44.56631;
    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 -149.8177, -123.2829;
    String axis "X";
    String ioos_category "Location";
    String long_name "Longitude";
    String standard_name "longitude";
    String units "degrees_east";
  }
  LibraryName {
    String long_name "Libraryname";
    String units "unitless";
  }
  LibraryLayout {
    String long_name "Librarylayout";
    String units "unitless";
  }
  LibrarySelection {
    String long_name "Libraryselection";
    String units "unitless";
  }
  LibrarySource {
    String long_name "Librarysource";
    String units "unitless";
  }
  Organism {
    String long_name "Organism";
    String units "unitless";
  }
  Platform {
    String long_name "Platform";
    String units "unitless";
  }
  ReleaseDate {
    String ioos_category "Time";
    String long_name "Releasedate";
    String time_origin "01-JAN-1970 00:00:00";
    String units "seconds since 1970-01-01T00:00:00Z";
  }
  create_date {
    String ioos_category "Time";
    String long_name "Create_date";
    String time_origin "01-JAN-1970 00:00:00";
    String units "seconds since 1970-01-01T00:00:00Z";
  }
  version {
    Int32 actual_range 1, 1;
    String long_name "Version";
    String units "unitless";
  }
  SRA_Study {
    String long_name "Sra_study";
    String units "unitless";
  }
  unique_sample_identifier {
    Int32 actual_range 1, 759;
    String long_name "Unique_sample_identifier";
    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.954262.1";
    Float64 Easternmost_Easting -123.2829;
    Float64 geospatial_lat_max 44.56631;
    Float64 geospatial_lat_min -17.4731;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -123.2829;
    Float64 geospatial_lon_min -149.8177;
    String geospatial_lon_units "degrees_east";
    String history 
"2025-08-02T04:06:10Z (local files)
2025-08-02T04:06:10Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_954262_v1.html";
    String infoUrl "https://osprey.bco-dmo.org/dataset/954262";
    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 44.56631;
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing -17.4731;
    String summary 
"This dataset contains the complete sample information for the 16S rRNA gene V4 region amplicon sequencing data associated with the NCBI SRA accession from BioProject PRJNA994532. All raw sequencing data can be found at this publicly available NCBI SRA BioProject. 

The associated samples were collected from an in situ coral manipulative experiment in Moorea, French Polynesia between 2018-2020 from Acropora retusa, Porites lobata, and Pocillopora spp. Data collection was a multi-university collaborative effort between the Vega Thurber Laboratory,  at Oregon State University during the time of the experiment, and the Burkepile Community Ecology Laboratory at UC Santa Barbara. The experiment, conducted on the fore reef on the north shore of the island, evaluated the interaction of consumer pressure level (termed \"Herbivory\" in the dataset and in Vompe et al., 2023) and nutrient enrichment on coral microbiome composition and host success. The experiment also captured two severe and sequential marine heatwaves in 2019 and 2020. This experiment aimed to  evaluate whether managing local inputs, including water column nutrient levels and fishing regimes, interacts with heat stress to affect coral success. Coral microbiomes were sampled as these microbial communities are known to interact with host health during heat stress. The data herein correspond to the microbiomes of the sampled corals.";
    String title "[RECHARGE 2018 - 2020 Microbiome Data] - Sequence read accession (SRA) numbers and collection metadata for coral microbiome collected in Moorea, French Polynesia from Jul 2018 to Aug 2020 (Collaborative Research: Tipping points in coral reefs and their associated microbiomes: interactive effects of herbivory, nutrient enrichment, and temperature)";
    Float64 Westernmost_Easting -149.8177;
  }
}

 

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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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