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Dataset Title:  Coral colony sizes and conditions, of three species of the Orbicella
complex (Orbicella annularis, O. faveolata and O. franksi) in two donor sites
of a reciprocal transplant experiment, Varadero and Punta Brava, 2017
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_786632)
Range: depth = 2.0 to 25.0m
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
 
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Things You Can Do With Your Graphs

Well, you can do anything you want with your graphs, of course. But some things you might not have considered are:

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Site {
    String bcodmo_name "site";
    String description "coral fragment donor site";
    String long_name "Site";
    String units "unitless";
  }
  depth {
    String _CoordinateAxisType "Height";
    String _CoordinateZisPositive "down";
    Float64 _FillValue NaN;
    Float64 actual_range 2.0, 25.0;
    String axis "Z";
    String bcodmo_name "depth";
    Float64 colorBarMaximum 8000.0;
    Float64 colorBarMinimum -8000.0;
    String colorBarPalette "TopographyDepth";
    String description "depth at which the survey was performed";
    String ioos_category "Location";
    String long_name "Depth";
    String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
    String positive "down";
    String standard_name "depth";
    String units "m";
  }
  Transect {
    Byte _FillValue 127;
    Byte actual_range 1, 5;
    String bcodmo_name "transect";
    String description "transect identifier";
    String long_name "Transect";
    String units "unitless";
  }
  taxon_code {
    String bcodmo_name "taxon_code";
    String description "Orbicella species code: Oann= O. annularis; Ofav= O. faveolata; Ofra= O. franksi";
    String long_name "Taxon Code";
    String units "unitless";
  }
  diam_max {
    Int16 _FillValue 32767;
    Int16 actual_range 10, 320;
    String bcodmo_name "diameter";
    String description "Longest diameter of the colony";
    String long_name "Diam Max";
    String units "centimeters";
  }
  diam_min {
    Int16 _FillValue 32767;
    Int16 actual_range 5, 300;
    String bcodmo_name "diameter";
    String description "Shortest diameter of the colony";
    String long_name "Diam Min";
    String units "centimeters";
  }
  height {
    Int16 _FillValue 32767;
    Int16 actual_range 2, 230;
    String bcodmo_name "height";
    String description "Height of the colony";
    String long_name "Height";
    String units "centimeters";
  }
  mortality_old {
    Byte _FillValue 127;
    Byte actual_range 0, 100;
    String bcodmo_name "unknown";
    String description "Visible old mortality of the coral tissue (percentage)";
    String long_name "Mortality Old";
    String units "unitless";
  }
  mortality_new {
    Byte _FillValue 127;
    Byte actual_range 0, 95;
    String bcodmo_name "unknown";
    String description "Visible recent mortality of the coral tissue (percentage)";
    String long_name "Mortality New";
    String units "unitless";
  }
  mortality_total {
    Byte _FillValue 127;
    Byte actual_range 0, 100;
    String bcodmo_name "unknown";
    String description "Total mortality (percentage)";
    String long_name "Mortality Total";
    String units "unitless";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"The Varadero Reef is located south-west of the Cartagena Bay close to the
southern strait that connects the Bay to the Caribbean Sea in Colombia. The
Bay is a receiving estuary from the Magdalena River through the Canal del
Dique, a man-made channel whose construction and operation dates back almost a
century. The bathymetric distribution of the Orbicella species complex was
evaluated at two reference sites with contrasting exposure to the Dique
channel freshwater plume: 1) Varadero reef close to the Dique channel mouth
(10\\u00b018\\u201923.3\\u201dN, 75\\u00b035\\u201908.0\\u201dW), and 2) Rosario
reef located 21 km southwest of Varadero, significantly less exposed to the
turbid plume from the Dique channel (10\\u00b011'12.1\\\"N, 75\\u00b044'43.0\\\"W).
 
To estimate the potential negative effect of perturbing the optical properties
of water and light penetration on coral survival, we performed ecological
surveys of Orbicella spp. populations. Populations were sampled along the
whole depth range at which Orbicella spp. were observed. Random dives near the
experimental sites allowed us to define the depth limits of distribution. The
number of colonies of each species was recorded on 10x1 m belt transects
deployed perpendicular to the reef slope at six depths in Varadero (2, 3, 4.5,
6, 7.5 and 9m) and eight in Rosario (3, 5, 7, 9, 13, 17, 21 and 25m). Colony
size (length D1, wide D2 and height H, in centimeters) and percentage of
mortality (both recent and old mortality, using the AGRAA protocol) were also
recorded at all transects.
 
A diving computer Leonardo Cressi Sub was used to determine the depths of
surveys. A 50m measuring tape was used to determine the length of the belt
transect. A 1m PVC pipe carried by the diver was used to determine the width
of each transect.";
    String awards_0_award_nid "717027";
    String awards_0_award_number "OCE-1642311";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1642311";
    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 
"Ecological survey data 2017: coral colony size and mortality at donor sites 
   For reciprocal transplant experiment of coral fragments from Varadero and Punta Brava reefs, May 2017 
   PI: M. Medina, R. Iglesias-Prieto, T. Lopez (Penn State) 
   version date: 2020-01-09";
    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 "2020-01-09T14:08:32Z";
    String date_modified "2020-03-04T21:42:14Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.786632.1";
    Float64 geospatial_vertical_max 25.0;
    Float64 geospatial_vertical_min 2.0;
    String geospatial_vertical_positive "down";
    String geospatial_vertical_units "m";
    String history 
"2020-08-06T12:35:29Z (local files)
2020-08-06T12:35:29Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_786632.das";
    String infoUrl "https://www.bco-dmo.org/dataset/786632";
    String institution "BCO-DMO";
    String instruments_0_acronym "Pressure Sensor";
    String instruments_0_dataset_instrument_description "Used to determine the depths of surveys.";
    String instruments_0_dataset_instrument_nid "786642";
    String instruments_0_description "A pressure sensor is a device used to measure absolute, differential, or gauge pressures.  It is used only when detailed instrument documentation is not available.";
    String instruments_0_instrument_name "Pressure Sensor";
    String instruments_0_instrument_nid "567";
    String instruments_0_supplied_name "Cressi Leonardo Scuba Dive Computer";
    String instruments_1_dataset_instrument_description "A 50m measuring tape was used to determine the length of the belt transect. A 1m PVC pipe carried by the diver was used to determine the width of each transect.";
    String instruments_1_dataset_instrument_nid "786643";
    String instruments_1_description "A tape measure or measuring tape is a flexible ruler. It consists of a ribbon of cloth, plastic, fibre glass, or metal strip with linear-measurement markings. It is a common measuring tool.";
    String instruments_1_instrument_name "Measuring Tape";
    String instruments_1_instrument_nid "645010";
    String keywords "bco, bco-dmo, biological, chemical, code, data, dataset, depth, diam, diam_max, diam_min, dmo, erddap, height, management, max, min, mortality, mortality_new, mortality_old, mortality_total, new, oceanography, office, old, preliminary, site, taxon, taxon_code, total, transect";
    String license "https://www.bco-dmo.org/dataset/786632/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/786632";
    String param_mapping "{'786632': {'Depth': 'master - depth'}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/786632/parameters";
    String people_0_affiliation "Pennsylvania State University";
    String people_0_affiliation_acronym "PSU";
    String people_0_person_name "Mónica Medina";
    String people_0_person_nid "472486";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Pennsylvania State University";
    String people_1_affiliation_acronym "PSU";
    String people_1_person_name "Roberto Iglesias-Prieto";
    String people_1_person_nid "717031";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "Pennsylvania State University";
    String people_2_affiliation_acronym "PSU";
    String people_2_person_name "Tomás Lopez Lodoño";
    String people_2_person_nid "732860";
    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 "Varadero Reef";
    String projects_0_acronym "Varadero Reef";
    String projects_0_description 
"NSF Award Abstract:
Coral reefs provide invaluable services to coastal communities, but coral populations worldwide are in a state of unprecedented decline. Studying resilient reefs is of primary importance for coral conservation and restoration efforts. A unique natural experiment in coral resilience to stress has been playing out in Cartagena Bay, Colombia since the Spanish conquistadors diverted the Magadalena River into the Bay in 1582. Varadero Reef at the southern mouth of the Bay has survived centuries of environmental insults and changing conditions with up to 80% coral cover. This reef provides an ideal system to test biological robustness theory. Given that Varadero is a highly perturbed system, we hypothesize that while likely more robust to perturbation than nearby pristine reefs, it will be less physiologically efficient. Some of the large star coral colonies (Orbicella faveolata) at this site have existed since before the construction of the Canal del Dique. These coral specimens contain invaluable information regarding the conditions of the Magdalena River wathershed and its construction in the XIV century. Changes in turbidity of the plume associated with the urban industrial and agricultural development of Colombia can be documented as variations in calcification rates and changes in the microstructure of the skeleton. The Colombian government has announced the approval for the construction of a shipping channel that will go right over this reef, with the goal to start dredging as early as Fall 2016 or early 2017. The RAPID funding mechanism would enable immediate collection of data and information of why this reef has survived centuries of environmental stress that can shed light on what genotype combinations of coral and its microbial constituents will fare better in similar conditions at other reef locations around the world. Coral reef conservation biology will benefit from this study by generating data for the development of stress diagnostic tools to identify resilient corals. This project will help broaden participation in science by training a diverse cohort of students to work effectively in the global arena while fostering productive collaborations with several Colombian researchers and educational institutions. Students will also gain cultural empathy and sensitivity through direct engagement with the members of society who are most directly impacted by coral reef degradation (e.g. fishermen). Student researchers from Penn State University will work alongside their Colombian counterparts to develop a series of bilingual blog posts to record the cultural and scientific aspects of this project's research expeditions. The blog postings will be submitted for wide dissemination to the Smithsonian's Ocean Portal where Penn State students have published in the past. An educational coral kit developed by the Medina Lab and extensively tested in schools in the US has been translated into Spanish and will be used in local schools in Cartagena and vicinities. All expedition data and metadata will be incorporated into the Global Coral Microbiome Project's interactive web portal, a responsive outreach tool allows researchers, students and/or teachers to access a wealth of information about every coral colony we sample and to virtually explore coral reefs around the world from any internet-enabled device.
This research will generate information to understand functional traits related to symbioses stability under different perturbation regimes. Comparative analyses of microbiome modifications generated during the reciprocal transplantation will allow us to document possible differential responses of the holobionts to acute and chronic stressors relative to corals not exposed to significant levels of perturbation. The development of local bio-optical models of coral calcification and the characterization of the coral holobiont will permit the distinction between the effects in calcification attributed to local turbidity from those that can be ;attributed to differences in host genotype and/or microbial community composition and function. The information recorded in coral skeletons can be used to reconstruct the rates of agricultural, industrial and urban development of Colombia through the last 5 centuries as changes in the turbidity of the effluent of the Magdalena River.";
    String projects_0_end_date "2018-06";
    String projects_0_geolocation "Caribbean Sea (10°18’10”N, 75°34’ 55”W)";
    String projects_0_name "RAPID: Coral robustness: lessons from an \"improbable\" reef";
    String projects_0_project_nid "717028";
    String projects_0_start_date "2016-07";
    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 "This dataset contains the primary data of the bathymetric survey of three species of the Orbicella complex (Orbicella annularis, O. faveolata and O. franksi). The surveys were performed in two donor sites of a reciprocal transplant experiment:  Varadero and Punta Brava. The number of colonies and some physiological traits recorded on a belt transect deployed perpendicular to the reef slope at a series of depths are reported.";
    String title "Coral colony sizes and conditions, of three species of the Orbicella complex (Orbicella annularis, O. faveolata and O. franksi) in two donor sites of a reciprocal transplant experiment, Varadero and Punta Brava, 2017";
    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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