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Dataset Title:  Database of oyster mortality based on body size treatment Subscribe RSS
Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_804502)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Files
 
Variable ?   Optional
Constraint #1 ?
Optional
Constraint #2 ?
   Minimum ?
 
   Maximum ?
 
 Plate_density (unitless) ?          "Full"    "Third"
 Plate_replicate (unitless) ?          "A"    "E"
 Cage_mesh_size (unitless) ?          "Large Mesh"    "Small Mesh"
 Oyster_size_treatment (unitless) ?          "L"    "SML"
 Individual_oyster_size (unitless) ?          "L"    "S"
 Individual_mortality (unitless) ?          0    1
 Mode_of_mortality (unitless) ?          "C"    "U"
 
Server-side Functions ?
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Plate_density {
    String bcodmo_name "sample_descrip";
    String description "Descriptor of the density of the experimental plate: Full (24 oysters per plate); Half (12 oysters per plate); Third (8 oysters per plate)";
    String long_name "Plate Density";
    String units "unitless";
  }
  Plate_replicate {
    String bcodmo_name "replicate";
    String description "Unique identifier for replicate plates within a given treatment";
    String long_name "Plate Replicate";
    String units "unitless";
  }
  Cage_mesh_size {
    String bcodmo_name "sample_descrip";
    String description "Descriptor of the mesh size used to surround each experimental plate: Small Mesh or Large Mesh";
    String long_name "Cage Mesh Size";
    String units "unitless";
  }
  Oyster_size_treatment {
    String bcodmo_name "sample_descrip";
    String description "Size treatment for the experimental plate: S (small oysters only); M (medium oysters only); L (large oysters only); SM (mix of small and medium oysters); SL (mix of small and large oysters); ML (mix of medium and large oysters); SML (mix of small, medium, and large oysters)";
    String long_name "Oyster Size Treatment";
    String units "unitless";
  }
  Individual_oyster_size {
    String bcodmo_name "sample_descrip";
    String description "Size class of each individual oyster on the experimental plate";
    String long_name "Individual Oyster Size";
    String units "unitless";
  }
  Individual_mortality {
    Byte _FillValue 127;
    Byte actual_range 0, 1;
    String bcodmo_name "sample_descrip";
    String description "Binomial code for the mortality of each individual oyster on the experimental plate: 0 (Alive) or 1 (Dead)";
    String long_name "Individual Mortality";
    String units "unitless";
  }
  Mode_of_mortality {
    String bcodmo_name "sample_descrip";
    String description "Category for the mode of mortality of each individual oyster: U (unknown); M (missing valve); D (drilled by a predator); C (crushed by a predator)";
    String long_name "Mode Of Mortality";
    String units "unitless";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"We utilised 10-month old oysters, spawned under the breeding program at the
Port Stephens Fisheries Institute (PSFI) in January 2015 and subsequently
grown out on nearby oyster leases, to establish three phenotypic treatments
with respect to size. The phenotypes were Small (mean size \\u00b1 SE; 18.88
\\u00b1 0.17 mm shell length), Medium (32.23 \\u00b10.21 mm shell length) and
Large (39.04 \\u00b1 0.32 mm shell length), with each phenotype receiving at
least 100 oysters from each of the same 16 family lines to produce treatments
of comparable genetic diversity.\\u00a0
 
Oysters were manipulated on concrete tiles that were deployed at a mid-
intertidal elevation along the eastern shoreline of Chowder Bay, Sydney
Harbour, Australia (33\\u00b050\\u201919.80\\u201dS,
151\\u00b015\\u201916.50\\u201dE).
 
Oyster phenotypic diversity (3 levels; 1, 2 or 3 size classes/tile) and
predator access (2 levels: small mesh cages and large mesh cages) were
manipulated in a fully orthogonal experiment on concrete tiles, measuring 30cm
(length) x 30cm (width) x 4cm (height). The large mesh was 2.5 cm in diameter.
The small mesh was 1.5 cm in diameter. In total we had 14 treatments: small
and large mesh cages containing small, medium and large oysters on their own,
all pairwise combinations, and all three phenotypes together. There were five
replicates per treatment, giving a total of 70 tiles.
 
Oysters were glued to concrete tiles using a 2-part epoxy adhesive (Megapoxy
HT, Permatech), with the various body sizes haphazardly interspersed on tiles
assigned to receive multiple phenotypes.\\u00a0 There was a 3 cm margin with no
oysters around each plate. No oysters died from this process.
 
Prior to caging of tiles, each was photographed (with a scale bar included) to
determine the initial size of all oysters and the position on each tile of the
various size classes.\\u00a0 We used maximum shell length along the
anterior\\u2013posterior axis as our measure of body size
 
Tiles were then enclosed within a box cage consisting of stainless steel mesh
of the assigned size. The tiles were not affixed to the mesh cage but sat on
the bottom of it. The mesh extended 10 cm above the surface of the tile. Mesh
was secured on the underside of the tile with cable ties.
 
Tiles were placed in Chowder Bay at the mid intertidal elevation at which
oysters naturally occur on 17th November 2015. Tiles were interspersed with
respect to treatment, separated by at least 0.5 m and wedged between boulders
to minimise flipping by waves. The tiles were sampled at 1 week and after 8
weeks (15 Jan 2016). At 1 week, three tiles were flipped by wave action but no
damage to oysters or cages were observed, so these were righted and secured in
new positions between boulders. No other flipping or damage to tiles was
recorded at the end of the experiment.";
    String awards_0_award_nid "709941";
    String awards_0_award_number "OCE-1652320";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1652320";
    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 awards_1_award_nid "805237";
    String awards_1_award_number "FT140100322";
    String awards_1_funder_name "Australian Research Council";
    String awards_1_funding_acronym "ARC";
    String awards_1_funding_source_nid "805236";
    String cdm_data_type "Other";
    String comment 
"Oyster mortality 
  PI: Randall Hughes  
  Data Version 1: 2020-03-02";
    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 "2020-03-02T14:10:50Z";
    String date_modified "2020-03-03T15:55:54Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.804502.1";
    String history 
"2021-10-21T10:41:49Z (local files)
2021-10-21T10:41:49Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_804502.html";
    String infoUrl "https://www.bco-dmo.org/dataset/804502";
    String institution "BCO-DMO";
    String keywords "bco, bco-dmo, biological, cage, Cage_mesh_size, chemical, data, dataset, density, dmo, erddap, individual, Individual_mortality, Individual_oyster_size, management, mesh, mode, Mode_of_mortality, mortality, oceanography, office, oyster, Oyster_size_treatment, plate, Plate_density, Plate_replicate, preliminary, replicate, size, treatment";
    String license "https://www.bco-dmo.org/dataset/804502/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/804502";
    String param_mapping "{'804502': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/804502/parameters";
    String people_0_affiliation "Northeastern University";
    String people_0_affiliation_acronym "NEU";
    String people_0_person_name "A. Randall Hughes";
    String people_0_person_nid "522929";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "University of New South Wales";
    String people_1_affiliation_acronym "UNSW";
    String people_1_person_name "Paul Gribben";
    String people_1_person_nid "804507";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "Woods Hole Oceanographic Institution";
    String people_2_affiliation_acronym "WHOI BCO-DMO";
    String people_2_person_name "Karen Soenen";
    String people_2_person_nid "748773";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "Seagrass and Oyster Ecosystems";
    String projects_0_acronym "Seagrass and Oyster Ecosystems";
    String projects_0_description 
"NSF Award Abstract:
Disease outbreaks in the ocean are increasing, causing losses of ecologically important marine species, but the factors contributing to these outbreaks are not well understood. This 5-year CAREER project will study disease prevalence and intensity in two marine foundation species - the seagrass Zostera marina and the Eastern oyster Crassostrea virginica. More specifically, host-disease relationships will be explored to understand how genetic diversity and population density of the host species impacts disease transmission and risk. This work will pair large-scale experimental restorations and smaller-scale field experiments to examine disease-host relationships across multiple spatial scales. Comparisons of patterns and mechanisms across the two coastal systems will provide an important first step towards identifying generalities in the diversity-density-disease relationship. To enhance the broader impacts and utility of this work, the experiments will be conducted in collaboration with restoration practitioners and guided by knowledge ascertained from key stakeholder groups. The project will support the development of an early career female researcher and multiple graduate and undergraduate students. Students will be trained in state-of-the-art molecular techniques to quantify oyster and seagrass parasites. Key findings from the surveys and experimental work will be incorporated into undergraduate courses focused on Conservation Biology, Marine Biology, and Disease Ecology. Finally, students in these courses will help develop social-ecological surveys and mutual learning games to stimulate knowledge transfer with stakeholders through a series of workshops.
The relationship between host genetic diversity and disease dynamics is complex. In some cases, known as a dilution effect, diversity reduces disease transmission and risk. However, the opposite relationship, known as the amplification effect, can also occur when diversity increases the risk of infection. Even if diversity directly reduces disease risk, simultaneous positive effects of diversity on host density could lead to amplification by increasing disease transmission between infected and uninfected individuals. Large-scale field restorations of seagrasses (Zostera marina) and oysters (Crassostrea virginica) will be utilized to test the effects of host genetic diversity on host population density and disease prevalence/intensity. Additional field experiments independently manipulating host genetic diversity and density will examine the mechanisms leading to dilution or amplification. Conducting similar manipulations in two marine foundation species - one a clonal plant and the other a non-clonal animal - will help identify commonalities in the diversity-density-disease relationship. Further, collaborations among project scientists, students, and stakeholders will enhance interdisciplinary training and help facilitate the exchange of information to improve management and restoration efforts. As part of these efforts, targeted surveys will be used to document the perceptions and attitudes of managers and restoration practitioners regarding genetic diversity and its role in ecological resilience and restoration.";
    String projects_0_end_date "2022-01";
    String projects_0_geolocation "Coastal New England";
    String projects_0_name "CAREER: Linking genetic diversity, population density, and disease prevalence in seagrass and oyster ecosystems";
    String projects_0_project_nid "709942";
    String projects_0_start_date "2017-02";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "Database of oyster mortality based on body size treatment";
    String title "Database of oyster mortality based on body size treatment";
    String version "1";
    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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