ERDDAP > tabledap > Data Access Form

Dataset Title:	[Metagenome sequencing samples] - Contextual data for samples collected for metagenome sequencing from the deep subseafloor biosphere as accessed via CORKs along the Juan de Fuca Ridge flank in the Northeast Pacific Ocean between 2008 and 2014 (Collaborative Research: Illuminating microbes and their viruses within the dark ocean crust through strain-level approaches)
Institution:	BCO-DMO   (Dataset ID: bcodmo_dataset_945915_v1)
Information:	Summary | License | FGDC | ISO 19115 | Metadata | Background | Files | Make a graph

 

Variable	Optional Constraint #1		Optional Constraint #2		Minimum	Maximum
Sample_Type (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Metagenome"	"Metagenome"
Sample_Name (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"JdFR08_20"	"JdFR14_NA29"
DNA_Isolation_Method (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"MoBio Powersoil"	"mixed"
Collection_Date (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"2008-08-07"	"2014-08-21"
Collection_Year (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		2008	2014
Collection_Month (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"August"	"September"
Collection_Day (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		3	31
Sample_Source (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"5 m from 1301B"	"Nearby CORK 1362B"
Fluid_Delivery_Line (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Tefzel"	"stainless steel"
Environment (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"seawater"	"subseafloor crusta..."
latitude (degrees_north)	!= =~ <= >= = < >		!= =~ <= >= = < >		47.75348	47.88745
longitude (degrees_east)	!= =~ <= >= = < >		!= =~ <= >= = < >		-128.6487	-127.7592
Depth (msb)	!= =~ <= >= = < >		!= =~ <= >= = < >		"0-48 msb"	"8-107 msb"
Area (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Pacific Ocean"	"Pacific Ocean"
Full_Sample_Name_and_Description (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Crustal fluids mic..."	"Sediment microbial..."
IMG_Genome_ID (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >
NCBI_Bioproject_Accession (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"PRJNA655006"	"PRJNA655107"
NCBI_Biosample_Accession (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SAMN15738681"	"SAMN15739102"
SRA_ID (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SRX9096344"	"SRX9096834"

 

Server-side Functions

distinct()

orderBy orderByDescending orderByClosest orderByCount orderByLimit orderByMax orderByMin orderByMinMax orderByMean orderBySum (" Sample_Type Sample_Name DNA_Isolation_Method Collection_Date Collection_Year Collection_Month Collection_Day Sample_Source Fluid_Delivery_Line Environment latitude longitude Depth Area Full_Sample_Name_and_Description IMG_Genome_ID NCBI_Bioproject_Accession NCBI_Biosample_Accession SRA_ID Sample_Type Sample_Name DNA_Isolation_Method Collection_Date Collection_Year Collection_Month Collection_Day Sample_Source Fluid_Delivery_Line Environment latitude longitude Depth Area Full_Sample_Name_and_Description IMG_Genome_ID NCBI_Bioproject_Accession NCBI_Biosample_Accession SRA_ID Sample_Type Sample_Name DNA_Isolation_Method Collection_Date Collection_Year Collection_Month Collection_Day Sample_Source Fluid_Delivery_Line Environment latitude longitude Depth Area Full_Sample_Name_and_Description IMG_Genome_ID NCBI_Bioproject_Accession NCBI_Biosample_Accession SRA_ID Sample_Type Sample_Name DNA_Isolation_Method Collection_Date Collection_Year Collection_Month Collection_Day Sample_Source Fluid_Delivery_Line Environment latitude longitude Depth Area Full_Sample_Name_and_Description IMG_Genome_ID NCBI_Bioproject_Accession NCBI_Biosample_Accession SRA_ID Sample_Type Sample_Name DNA_Isolation_Method Collection_Date Collection_Year Collection_Month Collection_Day Sample_Source Fluid_Delivery_Line Environment latitude longitude Depth Area Full_Sample_Name_and_Description IMG_Genome_ID NCBI_Bioproject_Accession NCBI_Biosample_Accession SRA_ID ")

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_Type {
    String long_name "Sample_type";
    String units "unitless";
  }
  Sample_Name {
    String long_name "Sample_name";
    String units "unitless";
  }
  DNA_Isolation_Method {
    String long_name "Dna_isolation_method";
    String units "unitless";
  }
  Collection_Date {
    String long_name "Collection_date";
    String units "unitless";
  }
  Collection_Year {
    Int32 actual_range 2008, 2014;
    String long_name "Collection_year";
    String units "unitless";
  }
  Collection_Month {
    String long_name "Collection_month";
    String units "unitless";
  }
  Collection_Day {
    Int32 actual_range 3, 31;
    String long_name "Collection_day";
    String units "unitless";
  }
  Sample_Source {
    String long_name "Sample_source";
    String units "unitless";
  }
  Fluid_Delivery_Line {
    String long_name "Fluid_delivery_line";
    String units "unitless";
  }
  Environment {
    String long_name "Environment";
    String units "unitless";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float32 actual_range 47.75348, 47.88745;
    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 -128.6487, -127.7592;
    String axis "X";
    String ioos_category "Location";
    String long_name "Longitude";
    String standard_name "longitude";
    String units "degrees_east";
  }
  Depth {
    String long_name "Depth";
    String units "msb";
  }
  Area {
    String long_name "Area";
    String units "unitless";
  }
  Full_Sample_Name_and_Description {
    String long_name "Full_sample_name_and_description";
    String units "unitless";
  }
  IMG_Genome_ID {
    String long_name "Img_genome_id";
    String units "unitless";
  }
  NCBI_Bioproject_Accession {
    String long_name "Ncbi_bioproject_accession";
    String units "unitless";
  }
  NCBI_Biosample_Accession {
    String long_name "Ncbi_biosample_accession";
    String units "unitless";
  }
  SRA_ID {
    String long_name "Sra_id";
    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.945915.1";
    Float64 Easternmost_Easting -127.7592;
    Float64 geospatial_lat_max 47.88745;
    Float64 geospatial_lat_min 47.75348;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -127.7592;
    Float64 geospatial_lon_min -128.6487;
    String geospatial_lon_units "degrees_east";
    String history 
"2025-01-31T04:32:41Z (local files)
2025-01-31T04:32:41Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_945915_v1.html";
    String infoUrl "https://www.bco-dmo.org/dataset/945915";
    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 47.88745;
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 47.75348;
    String summary "This dataset provides contextual information about samples used for metagenome sequencing. These samples were collected from pristine crustal fluids sampled via CORK observatories along the Juan de Fuca Ridge flank in the Northeast Pacific Ocean off the coast of North America. Also included are metadata for seawater and sediment metagenomes that have been sequenced as controls. All of the data are publicly available via the National Center for Biotechnology Information (NCBI) accession numbers provided in the dataset (BioProject numbers PRJNA655018 to PRJNA655040).";
    String title "[Metagenome sequencing samples] - Contextual data for samples collected for metagenome sequencing from the deep subseafloor biosphere as accessed via CORKs along the Juan de Fuca Ridge flank in the Northeast Pacific Ocean between 2008 and 2014 (Collaborative Research: Illuminating microbes and their viruses within the dark ocean crust through strain-level approaches)";
    Float64 Westernmost_Easting -128.6487;
  }
}

 

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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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