Accessing BCO-DMO data
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| Dataset Title: | [Belize core data] - Raw coral extension, density, and calcification data from Castillo lab research in Belize, 2009, 2012, and 2015 (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) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_734491) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
species {
String bcodmo_name "taxon_code";
String description "Atlantic and Gulf Rapid Reef Assessment (AGRRA) coral codes";
String long_name "Species";
String units "unitless";
}
species_code {
String bcodmo_name "taxon_code";
String description "code for taxonomic genus and species name.";
String long_name "Species Code";
String units "unitless";
}
core_ID {
String bcodmo_name "core_id";
String description "core sample identifier";
String long_name "Core ID";
String units "unitless";
}
site {
String bcodmo_name "site";
String description "site idenifier: nearby city name and reef zone";
String long_name "Site";
String units "unitless";
}
type {
String bcodmo_name "treatment";
String description "thermal regime code: 1=lowTP; 2=modTP; 3=highTP. These 3 categories are based on low; moderate; and high temperature parameters (see Baumann et al 2016 for details)";
String long_name "Type";
String units "unitless";
}
reef_zone {
String bcodmo_name "site_descrip";
String description "reef zone: ABR=atoll back reef ; AFR=atoll fore reef ; BR=back reef ; FR=fore reef ; NS=near shore";
String long_name "Reef Zone";
String units "unitless";
}
transect {
String bcodmo_name "transect";
String description "transect identifier";
String long_name "Transect";
String units "unitless";
}
core_diameter {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 2;
String bcodmo_name "diameter";
String description "diameter of core sample";
String long_name "Core Diameter";
String units "centimeters";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 16.0917, 18.000056;
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 -88.62881, -87.557139;
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 source_name "long";
String standard_name "longitude";
String units "degrees_east";
}
year_collected {
Int16 _FillValue 32767;
Int16 actual_range 2009, 2015;
String bcodmo_name "year";
String description "year sample was collected";
String long_name "Year Collected";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "unitless";
}
year_growth {
Int16 _FillValue 32767;
Int16 actual_range 1814, 2014;
String bcodmo_name "year";
String description "the year of growth referred to using CT images to line up banding patterns with years of growthyear of ?";
String long_name "Year Growth";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/";
String units "unitless";
}
density_g_cm3 {
Float32 _FillValue NaN;
Float32 actual_range 0.465814, 1.949521;
String bcodmo_name "density";
String description "density of coral core sample; available for 2015 samples only";
String long_name "Density G Cm3";
String units "grams/centimeter^3";
}
density_SE {
Float32 _FillValue NaN;
Float32 actual_range 0.00117, 0.403748;
String bcodmo_name "density";
String description "standard error of coral density";
String long_name "Density SE";
String units "grams/centimeter^3";
}
extension_cm {
Float32 _FillValue NaN;
Float32 actual_range 0.087167, 1.728411;
String bcodmo_name "growth";
String description "linear extension of each seasonal light and dark band pair in coral core";
String long_name "Extension Cm";
String units "centimeters";
}
extension_SE {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 0.467217;
String bcodmo_name "growth";
String description "standard error of extension values";
String long_name "Extension SE";
String units "centimeters";
}
calcification_g_cm2 {
Float32 _FillValue NaN;
Float32 actual_range 0.134786, 1.896251;
String bcodmo_name "calcification";
String description "calcification of coral core sample; available for 2015 samples only";
String long_name "Calcification G Cm2";
String units "grams/centimeter^2";
}
calc_SE {
Float32 _FillValue NaN;
Float32 actual_range 6.26e-4, 0.340249;
String bcodmo_name "calcification";
String description "standard error of calcification";
String long_name "Calc SE";
String units "grams/centimeter^2";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Coral core extraction
Cores were extracted by SCUBA divers using a pneumatic core drill [1] in 2009
or a hydraulic drill (Chicago Pneumatic COR 5 in 2012 or CS Unitec model 2
1335 0010, 3.8 HP) in 2015, both equipped with a 5 cm diameter diamond-tipped
core bit [1] Backreef S. siderea cores collected in 2015 were collected using
a pneumatic drill with a 2.5 cm diameter diamond-tipped core bit due to
permitting restrictions. All cores were extracted from colonies that appeared
healthy (i.e., no bleaching, abnormalities, scarring, or disease) near the
center of each colony. Cores were extracted parallel to the growth axis of
each colony and spanned the entire height of the colony, with the exception of
the backreef S. siderea cores collected in 2015 that ranged from 10-50
cm\\u2014spanning only the upper portion of the colony. Overall, core lengths
ranged from 10 cm to > 1 m. After extracting each core, a concrete plug was
inserted into the drilled hole and sealed with Z-spar underwater epoxy to
prevent bioerosion. Epoxy was only placed on the skeleton and the concrete to
avoid damage to the living tissue surrounding the hole. Cores were rinsed in
ethanol, stored in PVC tubes for transport, and transported to the University
of North Carolina at Chapel Hill for analysis. Collection permits were
obtained from the Belize Fisheries Department and all cores were collected and
transported pursuant to local, federal, and international regulations.
Coral CT Procedures
Coral cores collected in 2009 and 2012 were CT-scanned on a Siemens Somatom
Definition AS (120 kV, 300 mAs, 0.6 mm slice thickness) [2-4] at Wake
Radiology Chapel Hill in 2013 using methods modified from Carilli et al. [3]
and De\\u2019ath et al. [5]. Briefly, whole (i.e., unslabbed) cores were CT
scanned with the growth axis oriented perpendicular to the length of the CT
table. The resulting CT scans were uploaded to the DICOM viewing program
Osirix for further analysis following methods modified from Carilli et al.
[3]. Transects were drawn parallel to the core growth axis using the
\\u201clength\\u201d tool in Osirix. and within the exothecal space between
corallite walls in order to standardize density measurements between transects
and cores. Transects were performed in triplicate for each length of the core
in order to establish an average, exported to XML, and read into the program
RUNNINGCORALGUI, which identified the local density extrema (in Hounsfield
units) of the data in each XML file. The locations of these local extrema were
then quantified via pixel counting, with halfway points between local extrema
defining the boundaries of low and high-density bands. The number of pixels
between these halfway points and the average density in Hounsfield units was
quantified for the set of pixels between the halfway points. The linear
extension of each seasonal light and dark band was then quantified from the
total length of the line tool data in pixels, which was then converted to cm.
Coral cores from 2015 were CT scanned on a Siemens Biograph mCT (120 kV, 250
mAs, 0.6 mm slice thickness) at UNC Biomedical Research Imaging Center (BRIC).
CT images were reconstructed at 0.1 mm increments using the H70h \\u201cvery
sharp spine\\u201d window. All images were exported from the scanner as DICOM
files, which were then read into the medical image viewer Horos v2.0.2 (open-
source version of Osirix). Semiannual density bands were visualized using a
10-mm thick \\u201cMean\\u201d projection oriented through the center of the
core. In place of RUNNINGCORALGUI, all boundaries between high- and low-
density bands were delineated manually and three sets of linear transects were
drawn down the length of the cores using the ROI tool in Horos. Each set of
transects was drawn within the exothecal space between corallite walls in
order to standardize density measurements between cores and avoid abnormal
density spikes in areas where the transect crossed a high-density corallite
wall. By-pixel density measurements were then extracted from linear transects
and average density was calculated for each semiannual density band. Linear
extension (cm) was measured in Horos as the width of each density band, and
calcification (g/cm2) was calculated as the product of average density and
linear extension.
Coral core density standardization
Nine coral standards were used for density calibration. These standards were
pieces of various coral species from the Caribbean that had the same width as
the coral cores. Volume and mass of these standards were calculated with
calipers and a Mettler Toledo XPE205 analytical balance. Real-world density
for each standard was calculated as mass (determined by Mettler Toledo XPE205
analytical balance) divided by volume. The nine internal density standards
were scanned along with the cores at least once per scanning session (3-4
scans were completed during each 1-2 hour scanning session). A standard curve
was developed for each scanning session that related Houndsfield density
(measured from CT scan) to actual coral density (g/cm3), similar to DeCarlo et
al. [6].
1\\. Castillo et al (2011)
2. Saenger et al (2009)
3. Carilli et al (2012)
4. Cantin et al (2010)
5. De'ath G. et al (2009)
6. DeCarlo et al (2015)";
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
"Belize core data, 2009, 2012, 2015
raw extension, density, and calcification data
PI's: K. Castillo, J. Baumann
version: 2018-04-16";
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 "2018-04-26T14:14:18Z";
String date_modified "2019-12-12T16:11:48Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.734491.1";
Float64 Easternmost_Easting -87.557139;
Float64 geospatial_lat_max 18.000056;
Float64 geospatial_lat_min 16.0917;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -87.557139;
Float64 geospatial_lon_min -88.62881;
String geospatial_lon_units "degrees_east";
String history
"2024-11-08T06:02:10Z (local files)
2024-11-08T06:02:10Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_734491.html";
String infoUrl "https://www.bco-dmo.org/dataset/734491";
String institution "BCO-DMO";
String instruments_0_acronym "Drill Core";
String instruments_0_dataset_instrument_description "A pneumatic core drill or a hydraulic drill (Chicago Pneumatic COR 5 or CS Unitec model 2 1335 0010, 3.8 HP) with a 5 cm diameter diamond tipped core bit. Back reef S. siderea cores collected in 2015 were collected using a pneumatic drill with a 2.5 cm diameter diamond tipped core bit.";
String instruments_0_dataset_instrument_nid "734501";
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 "core drill";
String instruments_1_acronym "CT Scanner";
String instruments_1_dataset_instrument_description "Used to collect coral slice densities measurements.";
String instruments_1_dataset_instrument_nid "734500";
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 mCT (120 kV, 250 mAs, 0.6 mm slice thickness) at UNC Biomedical Research Imaging Center (BRIC)";
String keywords "bco, bco-dmo, biological, calc, calc_SE, calcification, calcification_g_cm2, chemical, cm2, cm3, code, collected, core, core_diameter, core_ID, data, dataset, density, density_g_cm3, density_SE, diameter, dmo, erddap, extension, extension_cm, extension_SE, growth, latitude, longitude, management, oceanography, office, preliminary, reef, reef_zone, site, species, species_code, transect, type, year, year_collected, year_growth, zone";
String license "https://www.bco-dmo.org/dataset/734491/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/734491";
Float64 Northernmost_Northing 18.000056;
String param_mapping "{'734491': {'lat': 'flag - latitude', 'long': 'flag - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/734491/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 "Justin Baumann";
String people_1_person_nid "733684";
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 "Justin Baumann";
String people_2_person_nid "733684";
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 16.0917;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "This dataset contains raw extension, density, and calcification data from corals sampled by the Castillo lab in Belize in 2009, 2012, and 2015.";
String title "[Belize core data] - Raw coral extension, density, and calcification data from Castillo lab research in Belize, 2009, 2012, and 2015 (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 version "1";
Float64 Westernmost_Easting -88.62881;
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
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.
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.