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Dataset Title:  Annual growth chronologies of Siderastrea siderea and Pseudodiploria strigosa
on the Florida Keys Reef Tract, 2015-2016
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_734706)
Range: longitude = -81.64903 to -80.09561°E, latitude = 24.495632 to 25.5919°N
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
 
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  species {
    String bcodmo_name "taxon_code";
    String description "Code for coral species sampled: ssid=Siderastrea siderea ; pstr=Pseudodiploria strigosa";
    String long_name "Species";
    String units "unitless";
  }
  reefZone {
    String bcodmo_name "site_descrip";
    String description "Inner vs outer reef";
    String long_name "Reef Zone";
    String units "unitless";
  }
  transect {
    String bcodmo_name "transect";
    String description "Inner-outer reef site pair: ir or or";
    String long_name "Transect";
    String units "unitless";
  }
  site {
    String bcodmo_name "site";
    String description "Sampling site identifier";
    String long_name "Site";
    String units "unitless";
  }
  coreID {
    String bcodmo_name "sample";
    String description "Unique identifier for each coral core";
    String long_name "Core ID";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
    String units "unitless";
  }
  latitude {
    String _CoordinateAxisType "Lat";
    Float64 _FillValue NaN;
    Float64 actual_range 24.495633, 25.5919;
    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 -81.64903, -80.09561;
    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";
  }
  year {
    Int16 _FillValue 32767;
    Int16 actual_range 1878, 2014;
    String bcodmo_name "year";
    String description "Year corresponding to each density band";
    String long_name "Year";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
    String units "unitless";
  }
  linext {
    Float32 _FillValue NaN;
    Float32 actual_range 0.1452, 1.0488;
    String bcodmo_name "growth";
    String description "Annual measurement of linear extension";
    String long_name "Linext";
    String units "centimeters/year (cm/yr)";
  }
  density {
    Float32 _FillValue NaN;
    Float32 actual_range 0.5112, 2.0577;
    String bcodmo_name "density";
    String description "Annual measurement of density";
    String long_name "Density";
    String units "grams/centimeter^3 (g/cm3)";
  }
  calc {
    Float32 _FillValue NaN;
    Float32 actual_range 0.1729, 1.1286;
    String bcodmo_name "calcification";
    String description "Annual measurement of calcification";
    String long_name "Calc";
    String units "grams/centimeter^2/year (g/cm2/yr)";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
    String acquisition_description 
"In May 2015 and 2016, skeletal cores were collected from 39 colonies of
Siderastrea siderea and 31 colonies of Pseudodiploria strigosa at four pairs
of inner-outer reef sites spanning the Florida Keys Reef Tract. All cores were
extracted from the vertical growth axis of each coral colony using a CS Unitec
model 2 1335 0010 hydraulic drill affixed with hollow extension rods and a 5
cm diameter wet diamond core bit. Collected cores were then stored in capped
PVC tubes filled with 100% EtOH and transported to the University of North
Carolina at Chapel Hill where they were air dried in preparation for
sclerochronology development. To assess coral skeletal growth histories, all
cores were scanned using X-ray computed tomography (CT) on a Siemens Biograph
CT scanner at the Biomedical Research Imaging Center, University of North
Carolina at Chapel Hill. Coral cores were oriented lengthwise in rows of 4 to
5 on the scanning table, and equipment parameters were set to 120 kV, 250 mAs
and 0.6 mm slice thickness with images reconstructed at 0.1 mm increments
using the H70h \\u201cVery Sharp Spine\\u201d window.
 
All images were exported from the CT scanner as DICOM files, which were then
3-dimensionally reconstructed using the open-access Horos v2.0.2 medical image
viewing software. High- and low-density bands were visualized using a 10-mm
thick \\u2018Mean\\u2019 projection oriented as a rectangular prism through the
center of each core. All boundaries between semiannual density bands were
delineated manually and three sets of linear transects were drawn down the
length of the cores using the Region of Interest (ROI) tool in Horos. Note,
each set of transects was drawn within the exothecal space between corallite
walls in order to standardize density measurements and to avoid aberrant
density spikes in areas where the transect may otherwise have crossed a high-
density corallite wall. Density and calcification measurements are therefore
lower than would be expected if all features of the skeletal architecture were
taken into account. Additionally, it has been shown that individual colonies
may vary in their timing of high- and low-density band deposition due to
intraspecific differences in tissue thickness and morphology (Barnes and
Lough, 1996; Carricart-Ganivet, 2013). Thus, to approximate a consistent time
standard between cores, we begin all chronologies at the top of the first
fully deposited density band beneath the band of terminal growth. By-pixel
density measurements were extracted from linear transects and average density
was calculated for each semiannual high- and low-density band. Following
DeCarlo et al (2015), nine coral standards of known density were included in
every scanning session to convert density measurements from CT Hounsfield
units to g cm-3. Average density of each standard was assessed in Hounsfield
units using Horos and a standard curve was created for all cores scanned in
the corresponding session. Linear extension (cm) was measured in Horos as the
width of each annual density band couplet, and calcification (g cm-2 yr-1) was
calculated as the product of density and linear extension.
 
Note, because cores were collected in subsequent years, the most recent year
of growth (2015) was not included for cores collected in 2016 in order to keep
the beginning of chronologies uniform throughout.
 
Analysis was based on previously published methods in Castillo et al (2011),
Castillo et al (2012).
 
\\u00a0";
    String awards_0_award_nid "635862";
    String awards_0_award_number "OCE-1459522";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1459522";
    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 
"Coral growth: 1878-2014 
     Florida Keys Reef Tract 
   PI's: K. Castillo, J. Rippe 
   version: 2018-04-30 
   NOTE: Species code list: <a href=\"https://datadocs.bco-dmo.org/docs/Thermal_History_Coral_Growth/data_docs/AGRRA_Coral_UW_Codes.pdf\" target=\"_blank\">AGRRA_Coral_UW_Codes.pdf</a>";
    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 "2018-04-30T19:45:33Z";
    String date_modified "2019-02-11T19:08:12Z";
    String defaultDataQuery "&amp;time&lt;now";
    String doi "10.1575/1912/bco-dmo.734706.1";
    Float64 Easternmost_Easting -80.09561;
    Float64 geospatial_lat_max 25.5919;
    Float64 geospatial_lat_min 24.495633;
    String geospatial_lat_units "degrees_north";
    Float64 geospatial_lon_max -80.09561;
    Float64 geospatial_lon_min -81.64903;
    String geospatial_lon_units "degrees_east";
    String history 
"2020-10-22T14:40:52Z (local files)
2020-10-22T14:40:52Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_734706.das";
    String infoUrl "https://www.bco-dmo.org/dataset/734706";
    String institution "BCO-DMO";
    String instruments_0_acronym "Drill Core";
    String instruments_0_dataset_instrument_description "Used to collect coral cores.";
    String instruments_0_dataset_instrument_nid "734714";
    String instruments_0_description 
"A core drill is a drill specifically designed to remove a cylinder of material, much like a hole saw. The material left inside the drill bit is referred to as the core.

Core drills are used frequently in mineral exploration where the coring may be several hundred to several thousand feet in length. The core samples are recovered and examined by geologists for mineral percentages and stratigraphic contact points. This gives exploration companies the information necessary to begin or abandon mining operations in a particular area.";
    String instruments_0_instrument_name "Drill Core";
    String instruments_0_instrument_nid "644572";
    String instruments_0_supplied_name "CS Unitec model 2 1335 0010 hydraulic core drill";
    String instruments_1_acronym "CT Scanner";
    String instruments_1_dataset_instrument_description "Used to collect coral slice densities measurements. Settings: 120 kV, 250 mAs, 0.6 mm slice thickness with images reconstructed at 0.1 mm increments using the H70h “Very Sharp Spine” window.";
    String instruments_1_dataset_instrument_nid "734713";
    String instruments_1_description "A CT scan makes use of computer-processed combinations of many X-ray measurements taken from different angles to produce cross-sectional (tomographic) images (virtual \"slices\") of specific areas of a scanned object.";
    String instruments_1_instrument_name "Computerized Tomography (CT) Scanner";
    String instruments_1_instrument_nid "707113";
    String instruments_1_supplied_name "Siemens Biograph CT scanner";
    String keywords "bco, bco-dmo, biological, calc, chemical, core, coreID, data, dataset, density, dmo, erddap, latitude, linext, longitude, management, oceanography, office, preliminary, reef, reefZone, site, species, transect, year, zone";
    String license "https://www.bco-dmo.org/dataset/734706/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/734706";
    Float64 Northernmost_Northing 25.5919;
    String param_mapping "{'734706': {'lat': 'master - latitude', 'lon': 'master - longitude'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/734706/parameters";
    String people_0_affiliation "University of North Carolina at Chapel Hill";
    String people_0_affiliation_acronym "UNC-Chapel Hill";
    String people_0_person_name "Karl D. Castillo";
    String people_0_person_nid "51711";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "University of North Carolina at Chapel Hill";
    String people_1_affiliation_acronym "UNC-Chapel Hill";
    String people_1_person_name "John P. Rippe";
    String people_1_person_nid "734717";
    String people_1_role "Student";
    String people_1_role_type "related";
    String people_2_affiliation "University of North Carolina at Chapel Hill";
    String people_2_affiliation_acronym "UNC-Chapel Hill";
    String people_2_person_name "John P. Rippe";
    String people_2_person_nid "734717";
    String people_2_role "Contact";
    String people_2_role_type "related";
    String people_3_affiliation "Woods Hole Oceanographic Institution";
    String people_3_affiliation_acronym "WHOI BCO-DMO";
    String people_3_person_name "Nancy Copley";
    String people_3_person_nid "50396";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "Thermal History and Coral Growth";
    String projects_0_acronym "Thermal History and Coral Growth";
    String projects_0_description 
"Description from NSF award abstract:
Rising global ocean surface temperatures have reduced coral growth rates, thereby negatively impacting the health of coral reef ecosystems worldwide. Recent studies on tropical reef building corals reveal that corals' growth in response to ocean warming may be influenced by their previous seawater temperature exposure - their thermal history. Although these recent findings highlight significant variability in coral growth in response to climate change, uncertainty remains as to the spatial scale at which corals' thermal history influences how they have responded to ocean warming and how they will likely respond to predicted future increases in ocean temperature. This study investigates the influence of thermal history on coral growth in response to recent and predicted seawater temperatures increases across four ecologically relevant spatial scales ranging from reef ecosystems, to reef communities, to reef populations, to an individual coral colony. By understanding how corals have responded in the past across a range of ecological scales, the Principal Investigator will be able to improve the ability to predict their susceptibility and resilience, which could then be applied to coral reef conservation in the face of climate change. This research project will broaden the participation of undergraduates from underrepresented groups and educate public radio listeners using minority voices and narratives. The scientist will leverage current and new partnerships to recruit and train minority undergraduates, thus allowing them to engage high school students near field sites in Florida, Belize, and Panama. Through peer advising, undergraduates will document this research on a digital news site for dissemination to the public. The voice of the undergraduates and scientist will ground the production of a public radio feature exploring the topic of acclimatization and resilience - a capacity for stress tolerance within coral reef ecosystems. This project will provide a postdoctoral researcher and several graduate students with opportunities for field and laboratory research training, teaching and mentoring, and professional development. The results will allow policy makers from Florida, the Mesoamerican Barrier Reef System countries, and several Central American countries to benefit from Caribbean-scale inferences that incorporate corals' physiological abilities, thereby improving coral reef management for the region.
Coral reefs are at significant risk due to a variety of local and global scale anthropogenic stressors. Although various stressors contribute to the observed decline in coral reef health, recent studies highlight rising seawater temperatures due to increasing atmospheric carbon dioxide concentration as one of the most significant stressors influencing coral growth rates. However, there is increasing recognition of problems of scale since a coral's growth response to an environmental stressor may be conditional on the scale of description. This research will investigate the following research questions: (1) How has seawater temperature on reef ecosystems (Florida Keys Reef Tract, USA; Belize Barrier Reef System, Belize; and Bocas Del Toro Reef Complex, Panama), reef communities (inshore and offshore reefs), reef populations (individual reefs), and near reef colonies (individual colonies), varied in the past? (2) How has seawater temperature influenced rates of coral growth and how does the seawater temperature-coral growth relationship vary across these four ecological spatial scales? (3) Does the seawater temperature-coral growth relationship forecast rates of coral growth under predicted end-of-century ocean warming at the four ecological spatial scales? Long term sea surface temperature records and small-scale high-resolution in situ seawater temperature measurements will be compared with growth chronologies for the reef building corals Siderastrea siderea and Orbicella faveolata, two keystone species ubiquitously distributed throughout the Caribbean Sea. Nutrients and irradiance will be quantified via satellite-derived observations, in situ measurements, and established colorimetric protocols. Field and laboratory experiments will be combined to examine seawater temperature-coral growth relationships under recent and predicted end-of-century ocean warming at four ecologically relevant spatial scales. The findings of this study will help us bridge the temperature-coral growth response gap across ecologically relevant spatial scales and thus improve our understanding of how corals have responded to recent warming. This will lead to more meaningful predictions about future coral growth response to climate change.";
    String projects_0_end_date "2018-02";
    String projects_0_geolocation "Western Caribbean";
    String projects_0_name "Investigating the influence of thermal history on coral growth response to recent and predicted end-of-century ocean warming across a cascade of ecological scales";
    String projects_0_project_nid "635863";
    String projects_0_project_website "http://www.unc.edu/~kdcastil/research.html";
    String projects_0_start_date "2015-03";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    Float64 Southernmost_Northing 24.495633;
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "This dataset includes annual measurements of extension, density, and calcification for 39 Siderastrea siderea cores and 31 Pseudodiploria strigosa cores from inner and outer reef sites spanning ~200 km of the Florida Keys Reef Tract.";
    String title "Annual growth chronologies of Siderastrea siderea and Pseudodiploria strigosa on the Florida Keys Reef Tract, 2015-2016";
    String version "1";
    Float64 Westernmost_Easting -81.64903;
    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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