ERDDAP > tabledap > Data Access Form

Dataset Title:	[Microbial eukaryotic diversity: Mid-Cayman Rise SRA dataset] - 18S rRNA amplicon sequencing of microbial eukaryotes from the Mid-Cayman Rise acquired Jan-Feb, 2020 (Probing subseafloor microbial interactions via hydrothermal vent fluids: A focus on protists)
Institution:	BCO-DMO   (Dataset ID: bcodmo_dataset_914399_v1)
Information:	Summary | License | Metadata | Background | Files | Make a graph

 

Variable	Optional Constraint #1		Optional Constraint #2		Minimum	Maximum
Experiment_Accession (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SRX14029944"	"SRX14029988"
Experiment_Title (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"18S rRNA gene ampl..."	"18S rRNA gene ampl..."
Organism_Name (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"hydrothermal vent ..."	"hydrothermal vent ..."
Instrument (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Illumina MiSeq"	"Illumina MiSeq"
Study_Accession (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SRP358043"	"SRP358043"
Study_Title (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"18S rRNA gene ampl..."	"18S rRNA gene ampl..."
Sample_Accession (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SRS11865559"	"SRS11865603"
Total_Size_Mb (Mb)	!= =~ <= >= = < >		!= =~ <= >= = < >
Total_Bases (bp)	!= =~ <= >= = < >		!= =~ <= >= = < >		375000	238791000
Library_Name (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"51_AGAGAA_S13"	"80_MCR_VonDamm_HOG..."
Library_Strategy (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"AMPLICON"	"AMPLICON"
Library_Source (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"METATRANSCRIPTOMIC"	"METATRANSCRIPTOMIC"
Library_Selection (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"PCR"	"PCR"
Vent_field (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Control"	"blank"
Collection (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"CTD"	"expTf"
Vent_name (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"ArrowLoop"	"shipboard"
DiveID (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"0"	"J21244HOG20"

 

Server-side Functions

distinct()

orderBy orderByDescending orderByClosest orderByCount orderByLimit orderByMax orderByMin orderByMinMax orderByMean orderBySum (" Experiment_Accession Experiment_Title Organism_Name Instrument Study_Accession Study_Title Sample_Accession Total_Size_Mb Total_Bases Library_Name Library_Strategy Library_Source Library_Selection Vent_field Collection Vent_name DiveID Experiment_Accession Experiment_Title Organism_Name Instrument Study_Accession Study_Title Sample_Accession Total_Size_Mb Total_Bases Library_Name Library_Strategy Library_Source Library_Selection Vent_field Collection Vent_name DiveID Experiment_Accession Experiment_Title Organism_Name Instrument Study_Accession Study_Title Sample_Accession Total_Size_Mb Total_Bases Library_Name Library_Strategy Library_Source Library_Selection Vent_field Collection Vent_name DiveID Experiment_Accession Experiment_Title Organism_Name Instrument Study_Accession Study_Title Sample_Accession Total_Size_Mb Total_Bases Library_Name Library_Strategy Library_Source Library_Selection Vent_field Collection Vent_name DiveID Experiment_Accession Experiment_Title Organism_Name Instrument Study_Accession Study_Title Sample_Accession Total_Size_Mb Total_Bases Library_Name Library_Strategy Library_Source Library_Selection Vent_field Collection Vent_name DiveID ")

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).

(Documentation / Bypass this form )
 
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Experiment_Accession {
    String long_name "Experiment_accession";
    String units "unitless";
  }
  Experiment_Title {
    String long_name "Experiment_title";
    String units "unitless";
  }
  Organism_Name {
    String long_name "Organism_name";
    String units "unitless";
  }
  Instrument {
    String long_name "Instrument";
    String units "unitless";
  }
  Study_Accession {
    String long_name "Study_accession";
    String units "unitless";
  }
  Study_Title {
    String long_name "Study_title";
    String units "unitless";
  }
  Sample_Accession {
    String long_name "Sample_accession";
    String units "unitless";
  }
  Total_Size_Mb {
    String long_name "Total_size_mb";
    String units "Mb";
  }
  Total_Bases {
    Int32 actual_range 375000, 238791000;
    String long_name "Total_bases";
    String units "bp";
  }
  Library_Name {
    String long_name "Library_name";
    String units "unitless";
  }
  Library_Strategy {
    String long_name "Library_strategy";
    String units "unitless";
  }
  Library_Source {
    String long_name "Library_source";
    String units "unitless";
  }
  Library_Selection {
    String long_name "Library_selection";
    String units "unitless";
  }
  Vent_field {
    String long_name "Vent_field";
    String units "unitless";
  }
  Collection {
    String long_name "Collection";
    String units "unitless";
  }
  Vent_name {
    String long_name "Vent_name";
    String units "unitless";
  }
  DiveID {
    String long_name "Diveid";
    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.914399.1";
    String history 
"2024-11-21T11:30:32Z (local files)
2024-11-21T11:30:32Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_914399_v1.html";
    String infoUrl "https://www.bco-dmo.org/dataset/914399";
    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.";
    String sourceUrl "(local files)";
    String summary "Single-celled microbial eukaryotes inhabit deep-sea hydrothermal vent environments and play critical ecological roles in the vent-associated microbial food web. 18S rRNA amplicon sequencing of diffuse venting fluids from two geochemically-distinct hydrothermal vent fields was applied to investigate community diversity patterns among protistan assemblages. Piccard and Von Damm vent fields are situated 20 km apart at the Mid-Cayman Rise in the Caribbean Sea. We describe species diversity patterns with respect to hydrothermal vent field and sample type, identify putative vent endemic microbial eukaryotes, and test how vent fluid geochemistry may influence microbial community diversity. Individual vent fields supported distinct and highly diverse assemblages of protists that included potentially endemic or novel vent-associated strains. This data adds to our growing knowledge of the biogeography of deep-sea microbial eukaryotes.";
    String title "[Microbial eukaryotic diversity: Mid-Cayman Rise SRA dataset] - 18S rRNA amplicon sequencing of microbial eukaryotes from the Mid-Cayman Rise acquired Jan-Feb, 2020 (Probing subseafloor microbial interactions via hydrothermal vent fluids: A focus on protists)";
  }
}

 

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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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