ERDDAP > tabledap > Data Access Form

Dataset Title:	[SRA archive of Magallana gigas] - NCBI accession numbers and related metadata for an SRA archive of the Pacific oyster, Magallana gigas (The genetic legacy of an Asian oyster introduction and its disease-causing parasite)
Institution:	BCO-DMO   (Dataset ID: bcodmo_dataset_958631_v1)
Information:	Summary | License | FGDC | ISO 19115 | Metadata | Background | Files | Make a graph

 

Variable	Optional Constraint #1		Optional Constraint #2		Minimum	Maximum
sample_name (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"AKK_01"	"YUR_26"
accession (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SRR29833510"	"SRR29834235"
bioproject_accession (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"PRJNA1135237"	"PRJNA1135237"
biosample_accession (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"SAMN42467452"	"SAMN42468177"
pop (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"AKK"	"YUR"
Population (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Akkeshi"	"Yura_Sumoto_HyogoP..."
Region (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Argentina"	"soCal"
Region2 (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Akkeshi"	"soEurope"
NatNon (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Introduced"	"Native"
Collection_Date (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"2005-07"	"2021-11"
CollectionMonth (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"August"	"September"
CollectionYear (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"2005"	"2021"
latitude (degrees_north)	!= =~ <= >= = < >		!= =~ <= >= = < >		-40.5394	58.8684
longitude (degrees_east)	!= =~ <= >= = < >		!= =~ <= >= = < >		-124.0237	175.11
Collector (unitless)	!= =~ <= >= = < >		!= =~ <= >= = < >		"Couceiro"	"Zacherl"

 

Server-side Functions

distinct()

orderBy orderByDescending orderByClosest orderByCount orderByLimit orderByMax orderByMin orderByMinMax orderByMean orderBySum (" sample_name accession bioproject_accession biosample_accession pop Population Region Region2 NatNon Collection_Date CollectionMonth CollectionYear latitude longitude Collector sample_name accession bioproject_accession biosample_accession pop Population Region Region2 NatNon Collection_Date CollectionMonth CollectionYear latitude longitude Collector sample_name accession bioproject_accession biosample_accession pop Population Region Region2 NatNon Collection_Date CollectionMonth CollectionYear latitude longitude Collector sample_name accession bioproject_accession biosample_accession pop Population Region Region2 NatNon Collection_Date CollectionMonth CollectionYear latitude longitude Collector sample_name accession bioproject_accession biosample_accession pop Population Region Region2 NatNon Collection_Date CollectionMonth CollectionYear latitude longitude Collector ")

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 )
 
Submit (Please be patient. It may take a while to get the data.)

 

---

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  sample_name {
    String long_name "Sample_name";
    String units "unitless";
  }
  accession {
    String long_name "Accession";
    String units "unitless";
  }
  bioproject_accession {
    String long_name "Bioproject_accession";
    String units "unitless";
  }
  biosample_accession {
    String long_name "Biosample_accession";
    String units "unitless";
  }
  pop {
    String long_name "Pop";
    String units "unitless";
  }
  Population {
    String long_name "Population";
    String units "unitless";
  }
  Region {
    String long_name "Region";
    String units "unitless";
  }
  Region2 {
    String long_name "Region2";
    String units "unitless";
  }
  NatNon {
    String long_name "Natnon";
    String units "unitless";
  }
  Collection_Date {
    String long_name "Collection_date";
    String units "unitless";
  }
  CollectionMonth {
    String long_name "Collectionmonth";
    String units "unitless";
  }
  CollectionYear {
    String long_name "Collectionyear";
    String units "unitless";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float32 actual_range -40.5394, 58.8684;
    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 -124.0237, 175.11;
    String axis "X";
    String ioos_category "Location";
    String long_name "Longitude";
    String standard_name "longitude";
    String units "degrees_east";
  }
  Collector {
    String long_name "Collector";
    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.958631.1";
    Float64 Easternmost_Easting 175.11;
    Float64 geospatial_lat_max 58.8684;
    Float64 geospatial_lat_min -40.5394;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max 175.11;
    Float64 geospatial_lon_min -124.0237;
    String geospatial_lon_units "degrees_east";
    String history 
"2025-04-20T13:40:37Z (local files)
2025-04-20T13:40:37Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_958631_v1.html";
    String infoUrl "https://osprey.bco-dmo.org/dataset/958631";
    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 58.8684;
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing -40.5394;
    String summary "The massive geographic expansion of terrestrial plant crops, livestock, and marine aquacultured species during the 19th and 20th centuries provided local economic benefits, stabilized food demands, and altered local ecosystems. The invasion history of these translocations remains uncertain for most species, limiting our understanding of their future adaptive potential and historical roles as vectors for co-invaded species. We provide a framework for filling this gap in invasion biology using the widely transplanted Pacific oyster (Magallana gigas) as a case study. A two-dimensional summary of population-level variation in single nucleotide polymorphisms (SNPs) in native Japan reflected the geographical map of Japan and allowed identification of the source regions for the worldwide expansion. Pacific oysters proliferate in non-native areas with environmental temperatures similar to those areas where native lineages evolved.";
    String title "[SRA archive of Magallana gigas] - NCBI accession numbers and related metadata for an SRA archive of the Pacific oyster, Magallana gigas (The genetic legacy of an Asian oyster introduction and its disease-causing parasite)";
    Float64 Westernmost_Easting -124.0237;
  }
}

 

---

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.

 

---

ERDDAP, Version 2.22
Disclaimers | Privacy Policy | Contact