Data Access Form

Dataset Title:	[RI Community Data] - An archive of the fish and inveterate data from the Rhode Island Department of Environmental Management (RIDEM) juvenile fin-fish survey across 6 Rhode Island salt ponds from 2010-2015 (CAREER: Linking genetic diversity, population density, and disease prevalence in seagrass and oyster ecosystems)
Institution:	BCO-DMO (Dataset ID: bcodmo_dataset_805252)
Information:	Summary \| License \| FGDC \| ISO 19115 \| Metadata \| Background \| Files \| Make a graph

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Variable	Minimum	Maximum
Year (unitless)	2010	2015
Pond (unitless)	"Green Hill"	"Winnapaug"
latitude (degrees_north)	41.3311	41.3998

longitude (degrees_east)	-71.7689	-71.5056

Common_Name (unitless)	"ALEWIFE"	"WINDOWPANE"
Scientific_Name (unitless)	"Albula vulpes"	"Urophycis tenuis"
Frequency (individuals)	1.0	3497.9

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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Year {
    Int16 _FillValue 32767;
    Int16 actual_range 2010, 2015;
    String bcodmo_name "year";
    String description "Year the organism was collected";
    String long_name "Year";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
    String units "unitless";
  }
  Pond {
    String bcodmo_name "site";
    String description "Name of pond where the organism was collected";
    String long_name "Pond";
    String units "unitless";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float64 _FillValue NaN;
    Float64 actual_range 41.3311, 41.3998;
    String axis "Y";
    String bcodmo_name "latitude";
    Float64 colorBarMaximum 90.0;
    Float64 colorBarMinimum -90.0;
    String description "Latitude of the pond";
    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 -71.7689, -71.5056;
    String axis "X";
    String bcodmo_name "longitude";
    Float64 colorBarMaximum 180.0;
    Float64 colorBarMinimum -180.0;
    String description "Longitude of the pond; negative values = West";
    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";
  }
  Common_Name {
    String bcodmo_name "common_name";
    String description "The scientific name of the organism to lowest taxonomic level possible";
    String long_name "Common Name";
    String units "unitless";
  }
  Scientific_Name {
    String bcodmo_name "species";
    String description "The common name of the organism";
    String long_name "Scientific Name";
    String units "unitless";
  }
  Frequency {
    Float32 _FillValue NaN;
    Float32 actual_range 1.0, 3497.9;
    String bcodmo_name "abundance";
    String description "The abundance of the organism collected. Frequency was calculated by summing individuals across stations within a pond per sampling event and averaging across year.";
    String long_name "Frequency";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
    String units "individuals";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
    String acquisition_description 
"Fish and invertebrate surveys:  
 The Rhode Island Department of Environmental Management (RIDEM) provided us
with the fish and invertebrate survey data for this study. Beginning in 2010,
RIDEM established permanent monitoring stations throughout all six coastal
ponds (points on Fig. 1A of Yeager et al., 2020). Communities were sampled
monthly from May to October each year via 150 ft beach seine net. Fish and
macroinvertebrate individuals were counted, measured, and identified to
species. Communities were composed of fishes and invertebrates from multiple
trophic levels. Across all ponds, species richness ranged from and 11 to 39
and trophic level ranged from 2.01 \\u2013 4.65 (Appendix S1 of Yeager et al.,
2020). For the community analysis, we examined species and their abundances
averaged across sampling stations to account for dependence within each pond
and averaged across months to account for seasonal differences of species
presence. To ensure even community sampling across ponds which varied in
number of sampling stations, we conducted a species rarefaction test,
examining both the rarefaction curves as well as the relationship between the
rarefied and observed number of species (Appendix S2 of Yeager et al., 2020).";
    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 cdm_data_type "Other";
    String comment 
"RI Community Data 
  PI: Mallarie Yeager (Northeastern University) 
  Co-PI: A. Randall Hughes (Northeastern University)  
  Version date: 03-March-2020";
    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 "2020-03-03T17:13:54Z";
    String date_modified "2020-03-12T13:28:14Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.1575/1912/bco-dmo.805252.1";
    Float64 Easternmost_Easting -71.5056;
    Float64 geospatial_lat_max 41.3998;
    Float64 geospatial_lat_min 41.3311;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -71.5056;
    Float64 geospatial_lon_min -71.7689;
    String geospatial_lon_units "degrees_east";
    String history 
"2024-12-03T17:40:38Z (local files)
2024-12-03T17:40:38Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_805252.html";
    String infoUrl "https://www.bco-dmo.org/dataset/805252";
    String institution "BCO-DMO";
    String instruments_0_dataset_instrument_nid "805256";
    String instruments_0_description 
"A seine net is a very long net, with or without a bag in the centre, which is set either from the shore or from a boat for surrounding a certain area and is operated with two (long) ropes fixed to its ends (for hauling and herding the fish).

Seine nets are operated both in inland and in marine waters. The surrounded and catching area depends on the length of the seine and of the hauling lines.

(definition from: fao.org)";
    String instruments_0_instrument_name "Seine Net";
    String instruments_0_instrument_nid "716403";
    String keywords "bco, bco-dmo, biological, chemical, common, Common_Name, data, dataset, dmo, erddap, frequency, latitude, longitude, management, name, oceanography, office, pond, preliminary, scientific, Scientific_Name, year";
    String license "https://www.bco-dmo.org/dataset/805252/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/805252";
    Float64 Northernmost_Northing 41.3998;
    String param_mapping "{'805252': {'Latitude': 'flag - latitude', 'Longitude': 'flag - longitude'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/805252/parameters";
    String people_0_affiliation "Northeastern University";
    String people_0_affiliation_acronym "NEU";
    String people_0_person_name "Mallarie Yeager";
    String people_0_person_nid "805269";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Northeastern University";
    String people_1_affiliation_acronym "NEU";
    String people_1_person_name "A. Randall Hughes";
    String people_1_person_nid "522929";
    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 "Shannon Rauch";
    String people_2_person_nid "51498";
    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)";
    Float64 Southernmost_Northing 41.3311;
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "An archive of the fish and inveterate data from the Rhode Island Department of Environmental Management (RIDEM) juvenile fin-fish survey across 6 Rhode Island salt ponds from 2010-2015.";
    String title "[RI Community Data] - An archive of the fish and inveterate data from the Rhode Island Department of Environmental Management (RIDEM) juvenile fin-fish survey across 6 Rhode Island salt ponds from 2010-2015 (CAREER: Linking genetic diversity, population density, and disease prevalence in seagrass and oyster ecosystems)";
    String version "1";
    Float64 Westernmost_Easting -71.7689;
    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.

(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.