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Dataset Title:  NCBI accessions and metadata associated with Caribbean sponge metagenomes
collected from Curacao, Belize, Cayman Islands and St. Croix, 2009 and 2017-2018
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_775451)
Information:  Summary ? | License ? | Metadata | Background (external link) | Subset | Files | Make a graph
 
Variable ?   Optional
Constraint #1 ?
Optional
Constraint #2 ?
   Minimum ?
   or a List of Values ?
   Maximum ?
 
 BioProject (unitless) ?      
   - +  ?
 BioSample (unitless) ?          "SAMN12290052"    "SAMN12291705"
 Sample_name (unitless) ?          "BZ001"    "agc60-1"
 sample_type (unitless) ?          "seawater metagenome"    "sponge metagenome"
 host (unitless) ?          "Aaptos"    "sediment"
 collection_date (unitless) ?          "1-Feb-18"    "9-Jul-18"
 geographic_location (unitless) ?          "Belize: Carrie Bow..."    "USA: St. Croix"
 latitude (degrees_north) ?          12.0828    19.4023
  < slider >
 longitude (degrees_east) ?          -88.0878    -64.673501
  < slider >
 source_material_identifiers (unitless) ?          "CJH-KY327"    "merged-CU211"
 depth_ (feet seawater (fsw) or meters) ?              
 
Server-side Functions ?
 distinct() ?
? ("Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.Hover here to see a list of options. Click on an option to select it.")

File type: (more info)

(Documentation / Bypass this form ? )
 
(Please be patient. It may take a while to get the data.)


 

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  BioProject {
    String bcodmo_name "accession number";
    String description "NCBI BioProject accession number";
    String long_name "Bio Project";
    String units "unitless";
  }
  BioSample {
    String bcodmo_name "accession number";
    String description "NCBI BioSample accession number";
    String long_name "Bio Sample";
    String units "unitless";
  }
  Sample_name {
    String bcodmo_name "sample";
    String description "Lab sample name";
    String long_name "Sample Name";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  }
  sample_type {
    String bcodmo_name "sample_descrip";
    String description "sample type and genomic analysis";
    String long_name "Sample Type";
    String units "unitless";
  }
  host {
    String bcodmo_name "taxon";
    String description "host taxon";
    String long_name "Host";
    String units "unitless";
  }
  collection_date {
    String bcodmo_name "date";
    String description "date collected";
    String long_name "Collection Date";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
    String units "unitless";
  }
  geographic_location {
    String bcodmo_name "site";
    String description "geographic location of collection";
    String long_name "Geographic Location";
    String units "unitless";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float64 _FillValue NaN;
    Float64 actual_range 12.0828, 19.4023;
    String axis "Y";
    String bcodmo_name "latitude";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "latitude; north is positive";
    String ioos_category "Location";
    String long_name "Latitude";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
    String standard_name "latitude";
    String units "degrees_north";
  }
  longitude {
    String _CoordinateAxisType "Lon";
    Float64 _FillValue NaN;
    Float64 actual_range -88.0878, -64.673501;
    String axis "X";
    String bcodmo_name "longitude";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "longitude; east is positive";
    String ioos_category "Location";
    String long_name "Longitude";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
    String standard_name "longitude";
    String units "degrees_east";
  }
  source_material_identifiers {
    String bcodmo_name "sample";
    String description "sample identifier";
    String long_name "Source Material Identifiers";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  }
  depth_ {
    Float64 _FillValue NaN;
    String bcodmo_name "depth";
    String description "collection depth guage measurement";
    String long_name "Depth";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
    String standard_name "depth";
    String units "feet seawater (fsw) or meters";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
    String acquisition_description "\"\"";
    String awards_0_award_nid "649060";
    String awards_0_award_number "OCE-1638296";
    String awards_0_data_url "https://www.nsf.gov/awardsearch/showAward?AWD_ID=1638296";
    String awards_0_funder_name "NSF Division of Ocean Sciences";
    String awards_0_funding_acronym "NSF OCE";
    String awards_0_funding_source_nid "355";
    String awards_0_program_manager "Michael E. Sieracki";
    String awards_0_program_manager_nid "50446";
    String cdm_data_type "Other";
    String comment 
"Sponge holobiont NCBI accessions and metadata for DoB biodiversity project 
   collections from Curacao, Belize, Cayman Islands and St. Croix, 2009 and 2017-2018 
   PI: M. Lesser (UNH), M. Slattery (Umiss) 
   version date: 2019-08-15 
   NOTE: These data were downloaded from NCBI BioProject PRJNA555077 on 2019-08-14 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA555077]";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_type "institution";
    String creator_url "https://www.bco-dmo.org/";
    String data_source "extract_data_as_tsv version 2.3  19 Dec 2019";
    String date_created "2019-08-15T19:42:23Z";
    String date_modified "2019-08-19T13:16:33Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.1575/1912/bco-dmo.775451.1";
    Float64 Easternmost_Easting -64.673501;
    Float64 geospatial_lat_max 19.4023;
    Float64 geospatial_lat_min 12.0828;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -64.673501;
    Float64 geospatial_lon_min -88.0878;
    String geospatial_lon_units "degrees_east";
    String history 
"2021-11-29T05:38:11Z (local files)
2021-11-29T05:38:11Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_775451.html";
    String infoUrl "https://www.bco-dmo.org/dataset/775451";
    String institution "BCO-DMO";
    String instruments_0_acronym "Automated Sequencer";
    String instruments_0_dataset_instrument_nid "775458";
    String instruments_0_description "General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.";
    String instruments_0_instrument_name "Automated DNA Sequencer";
    String instruments_0_instrument_nid "649";
    String instruments_1_acronym "Light Meter";
    String instruments_1_dataset_instrument_nid "775508";
    String instruments_1_description "Light meters are instruments that measure light intensity. Common units of measure for light intensity are umol/m2/s or uE/m2/s (micromoles per meter squared per second or microEinsteins per meter squared per second). (example: LI-COR 250A)";
    String instruments_1_instrument_name "Light Meter";
    String instruments_1_instrument_nid "703";
    String instruments_1_supplied_name "in situ light sensor";
    String instruments_2_dataset_instrument_nid "775507";
    String instruments_2_instrument_name "Thermometer";
    String instruments_2_instrument_nid "725867";
    String instruments_2_supplied_name "in situ temperature sensor";
    String keywords "bco, bco-dmo, bio, biological, BioProject, BioSample, chemical, collection, collection_date, data, dataset, date, depth, depth2, dmo, erddap, geographic, geographic_location, host, identifiers, latitude, longitude, management, material, name, oceanography, office, preliminary, project, sample, Sample_name, sample_type, source, source_material_identifiers, type";
    String license "https://www.bco-dmo.org/dataset/775451/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/775451";
    Float64 Northernmost_Northing 19.4023;
    String param_mapping "{'775451': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/775451/parameters";
    String people_0_affiliation "University of New Hampshire";
    String people_0_affiliation_acronym "UNH";
    String people_0_person_name "Dr Michael P. Lesser";
    String people_0_person_nid "645511";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "University of Mississippi";
    String people_1_person_name "Dr Marc Slattery";
    String people_1_person_nid "647901";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String project "DimensionsSponge";
    String projects_0_acronym "DimensionsSponge";
    String projects_0_description 
"NSF Award Abstract:
Coral reefs, the tropical rain forests of the marine environment, are under significant threat from a variety of stressors such as pollution, overfishing, coastal development and climate change. There is increasing interest by the coral reef research community in the ecology and evolution of other groups of organisms besides corals on coral reefs with sponges being of particular interest. Sponges are a very old group of organisms essential to reef health because of their roles in nutrient cycling, providing food and homes for many other reef organisms, and their ability to synthesize diverse chemical compounds of ecological importance on the reef, and of interest to the biomedical community. Many of these important functions would not be possible without the symbiotic microbes (e.g., bacteria) that live within sponges. In this project, the investigators will examine relationships between the sponge host and its microbiome in the ecological roles described above. Like the human microbiome, understanding the sponge micobiome may be the key to understanding their ecology and biodiversity. The investigators will use a combination of classical ecological approaches combined with sophisticated biochemical and molecular analyses to unravel the role of the symbionts in the ecology and evolution of sponges. Both the University of New Hampshire and the University of Mississippi will provide training opportunities for undergraduate and graduate students as well as veterans and post-doctoral researchers, especially from underrepresented groups. Additionally, the investigators will develop unique outreach programs for public education on the importance of coral reef ecosystems.
The goal of this study is to examine the relationships between marine sponges and their microbiomes, and reveal the phylogenetic, genetic, and functional biodiversity of coral reef sponges across the Caribbean basin. This research will provide a better understanding of sponges as a major functional component of the biodiversity of coral reef communities. This transformative project will examine important paradigms relative to sponge communities worldwide that will provide unique insights into the integrative biodiversity of sponges on coral reefs and enhance our understanding of the ecology and evolution of this extensive, yet understudied, group of marine organisms. This is essential because sponges continue to emerge as the dominant taxon on many coral reefs, particularly following regional declines in coral cover over the last three decades, and their ecological importance to shallow coral reef communities is unequivocal. In addition, many marine sponges host a diverse assemblage of symbiotic microorganisms that play critical functional roles in nutrient cycling within sponges themselves and in the coral reef communities where they reside, and many sponges can potentially transfer photoautotrophically derived energy to higher trophic levels. As shallow coral reefs continue to decline, the phylogenetic, genetic, and functional diversity of coral reefs will increasingly be found in taxa other than scleractinian corals, such as soft corals and sponges. The investigators predict that co-evolution of the sponge host and microbiome leads to emergent functional properties that result in niche diversification and speciation of sponges. To assess this, they will quantify trophic modes (e.g., DOM and POC uptake, photo-autotrophy) of sponges in the Caribbean, as well as the production of chemical defenses. These character states will be analyzed in the context of the phylogenetic composition of the sponge hosts and their microbiomes, and the functional activities of the host and symbionts at the genetic level (i.e., transcriptomics and metatranscriptomics). These data will provide unique insights into the co-evolution of sponges and their microbiomes, and how these symbioses influence the functional attributes of sponges within coral reef communities.";
    String projects_0_end_date "2019-09";
    String projects_0_geolocation "Curacao, Belize, Florida, Cayman Islands";
    String projects_0_name "Collaborative Research: Dimensions: Evolutionary Ecology of Sponges and Their Microbiome Drives Sponge Diversity on Coral Reefs";
    String projects_0_project_nid "649062";
    String projects_0_start_date "2016-10";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 12.0828;
    String standard_name_vocabulary "CF Standard Name Table v55";
    String subsetVariables "BioProject";
    String summary "NCBI accessions and metadata associated with Caribbean sponge metagenomes collected from Curacao, Belize, Cayman Islands and St. Croix, 2009 and 2017-2018.";
    String title "NCBI accessions and metadata associated with Caribbean sponge metagenomes collected from Curacao, Belize, Cayman Islands and St. Croix, 2009 and 2017-2018";
    String version "1";
    Float64 Westernmost_Easting -88.0878;
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

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 (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

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.

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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