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Dataset Title:  Calcification of coral from the start and end of experiments under elevated
concentrations of temperature and carbon dioxide
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_748383)
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 {
  Coral_number {
    Byte _FillValue 127;
    Byte actual_range 1, 48;
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "Unique coral colony identification number";
    String ioos_category "Statistics";
    String long_name "Coral Number";
    String units "unitless";
  }
  pH {
    Float64 colorBarMaximum 9.0;
    Float64 colorBarMinimum 7.0;
    String description "pH treatment";
    String ioos_category "Salinity";
    String long_name "Sea Water Ph Reported On Total Scale";
    String units "unitless";
  }
  Temperature {
    String description "Temperature treatment";
    String ioos_category "Temperature";
    String long_name "Temperature";
    String units "unitless";
  }
  Crab {
    String description "Crab treatment: with (Yes) or without (No)";
    String ioos_category "Unknown";
    String long_name "Crab";
    String units "unitless";
  }
  Growth {
    Float64 _FillValue NaN;
    Float64 actual_range -0.01751436, 0.556493305;
    String description "Change in weight (g) obtained by buoyant weighing pre and post experiment, and later converted to mass of CaCO3 and normalized to surface area of coral tissue (Stimson and Kinzie 1991).";
    String ioos_category "Unknown";
    String long_name "Growth";
    String units "grams";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Collection and experimental setup methods extracted from Doo et al. (2018):  
 Colony collection: In January 2017, 48 colonies of Pocillopora verrucosa
(Ellis and Solander 1786) were collected randomly on scuba from 5 m depth on
the north shore of Mo\\u2019orea, French Polynesia (17\\u00b0 28'\\u00a033\\\"S,
149\\u00b0 49' 20\\\"W).\\u00a0Following 5 d of acclimation, 24 of the corals were
selected randomly for removal of all trapeziid crabs and alpheid shrimps\\u00a0
(\\\"minus-ectosymbiont\\\") by probing with a wooden stick (3 mm diameter). Crabs
and shrimp were left in the other 24 corals (\\\"plus-ectosymbiont\\\"), which
were subjected to a procedural control in which they were probed with a wooden
stick.
 
Incubation setup:\\u00a0Twelve mesocosm tanks (150 L volume with sand-filtered
seawater pumped from 14 m depth in Cooks\\u2019 Bay and supplied to the tanks
at ~200 mL min\\u22121) were used in this experiment, with four colonies per
tank in a split-plot design contrasting plus-ectosymbiont (n = 2
colonies/tank) and minus-ectosymbiont (n = 2 colonies/tank) corals.
 
Daily measures of salinity, pH, and total alkalinity (TA):\\u00a0  
 Temperature was recorded with a thermometer (\\u00b1 0.05 degrees C;
ThermoFisher Traceable) and salinity was measured with a bench-top
conductivity meter (\\u00b1 0.1 psu, YSI 3100). TA and pH were measured within
one hour of sample collection. Seawater collected for TA was filtered (0.45
um; Chanson and Millero, 2007) and analyzed using potentiometric titrations
with 0.1-N HCl using an automatic titrator (Mettler Toledo T50) (Dickson et
al., 2007). Seawater pH was measured with spectrophotometric methods (Nemzer
and Dickson, 2005).
 
Buoyant weight:\\u00a0was measured at start and end of experiment and
difference between the two values was used to calculate an increase in dry
skeletal weight (i.e., calcification) using the density of aragonite, and then
normalized to the surface area of each coral (Davies 1989).";
    String awards_0_award_nid "520630";
    String awards_0_award_number "OCE-1026851";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1026851";
    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 "Dr David  L. Garrison";
    String awards_0_program_manager_nid "50534";
    String awards_1_award_nid "526719";
    String awards_1_award_number "OCE-1236905";
    String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1236905";
    String awards_1_funder_name "NSF Division of Ocean Sciences";
    String awards_1_funding_acronym "NSF OCE";
    String awards_1_funding_source_nid "355";
    String awards_1_program_manager "Dr David  L. Garrison";
    String awards_1_program_manager_nid "50534";
    String awards_2_award_nid "536317";
    String awards_2_award_number "OCE-1415268";
    String awards_2_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1415268";
    String awards_2_funder_name "NSF Division of Ocean Sciences";
    String awards_2_funding_acronym "NSF OCE";
    String awards_2_funding_source_nid "355";
    String awards_2_program_manager "Dr David  L. Garrison";
    String awards_2_program_manager_nid "50534";
    String cdm_data_type "Other";
    String comment 
"Doo et al. 2018, Coral Reefs - Mesocosm buoyant weight data 
  PI: Robert Carpenter (CSUN) 
  Co-PI: Peter Edmunds (CSUN) 
  Contact: Steve Doo (CSUN) 
  Version date: 16 October 2018";
    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.pl v1.0";
    String date_created "2018-10-17T17:19:09Z";
    String date_modified "2019-03-15T16:33:54Z";
    String defaultDataQuery "&time";
    String doi "10.1575/1912/bco-dmo.748383.1";
    String history 
"2019-06-16T02:28:08Z (local files)
2019-06-16T02:28:08Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_748383.das";
    String infoUrl "https://www.bco-dmo.org/dataset/748383";
    String institution "BCO-DMO";
    String instruments_0_acronym "Scale";
    String instruments_0_dataset_instrument_nid "748454";
    String instruments_0_description "An instrument used to measure weight or mass.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB13/";
    String instruments_0_instrument_name "Scale";
    String instruments_0_instrument_nid "714";
    String instruments_0_supplied_name "Mettler PB153-S balance";
    String keywords "bco, bco-dmo, biological, chemical, chemistry, coral, Coral_number, crab, data, dataset, dmo, earth, Earth Science > Oceans > Ocean Chemistry > pH, erddap, growth, management, number, ocean, oceanography, oceans, office, preliminary, reported, salinity, scale, science, sea, sea_water_ph_reported_on_total_scale, seawater, statistics, temperature, total, water";
    String keywords_vocabulary "GCMD Science Keywords";
    String license 
"The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.";
    String metadata_source "https://www.bco-dmo.org/api/dataset/748383";
    String param_mapping "{'748383': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/748383/parameters";
    String people_0_affiliation "California State University Northridge";
    String people_0_affiliation_acronym "CSU-Northridge";
    String people_0_person_name "Robert Carpenter";
    String people_0_person_nid "51535";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "California State University Northridge";
    String people_1_affiliation_acronym "CSU-Northridge";
    String people_1_person_name "Peter J. Edmunds";
    String people_1_person_nid "51536";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "California State University Northridge";
    String people_2_affiliation_acronym "CSU-Northridge";
    String people_2_person_name "Steve Doo";
    String people_2_person_nid "748154";
    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 "Shannon Rauch";
    String people_3_person_nid "51498";
    String people_3_role "BCO-DMO Data Manager";
    String people_3_role_type "related";
    String project "Moorea Coral Reef Long-Term Ecological Research site, Collaborative Research: Ocean Acidification and Coral Reefs: Scale Dependence and Adaptive Capacity";
    String projects_0_acronym "MCR LTER";
    String projects_0_description 
"From http://www.lternet.edu/sites/mcr/ and http://mcr.lternet.edu/:
The Moorea Coral Reef LTER site encompasses the coral reef complex that surrounds the island of Moorea, French Polynesia (17�30'S, 149�50'W). Moorea is a small, triangular volcanic island 20 km west of Tahiti in the Society Islands of French Polynesia. An offshore barrier reef forms a system of shallow (mean depth ~ 5-7 m), narrow (~0.8-1.5 km wide) lagoons around the 60 km perimeter of Moorea. All major coral reef types (e.g., fringing reef, lagoon patch reefs, back reef, barrier reef and fore reef) are present and accessible by small boat.
The MCR LTER was established in 2004 by the US National Science Foundation (NSF) and is a partnership between the University of California Santa Barbara and California State University, Northridge. MCR researchers include marine scientists from the UC Santa Barbara, CSU Northridge, UC Davis, UC Santa Cruz, UC San Diego, CSU San Marcos, Duke University and the University of Hawaii. Field operations are conducted from the UC Berkeley Richard B. Gump South Pacific Research Station on the island of Moorea, French Polynesia.
MCR LTER Data: The Moorea Coral Reef (MCR) LTER data are managed by and available directly from the MCR project data site URL shown above.� The datasets listed below were collected at or near the MCR LTER sampling locations, and funded by NSF OCE as ancillary projects related to the MCR LTER core research themes.
The following publications and data resulted from this project:
2012 Edmunds PJ. Effect of pCO2 on the growth, respiration, and photophysiology of massive Porites spp. in Moorea, French Polynesia. Marine Biology 159: 2149-2160. doi:10.1594/PANGAEA.820375Porites growth_respiration_photophysDownload complete data for this publication (Excel file)";
    String projects_0_geolocation "Island of Moorea, French Polynesia";
    String projects_0_name "Moorea Coral Reef Long-Term Ecological Research site";
    String projects_0_project_nid "2222";
    String projects_0_project_website "http://mcr.lternet.edu/";
    String projects_0_start_date "2004-09";
    String projects_1_acronym "OA coral adaptation";
    String projects_1_description 
"Extracted from the NSF award abstract:
This project focuses on the most serious threat to marine ecosystems, Ocean Acidification (OA), and addresses the problem in the most diverse and beautiful ecosystem on the planet, coral reefs. The research utilizes Moorea, French Polynesia as a model system, and builds from the NSF investment in the Moorea Coral Reef Long Term Ecological Research Site (LTER) to exploit physical and biological monitoring of coral reefs as a context for a program of studies focused on the ways in which OA will affect corals, calcified algae, and coral reef ecosystems. The project builds on a four-year NSF award with research in five new directions: (1) experiments of year-long duration, (2) studies of coral reefs to 20-m depth, (3) experiments in which carbon dioxide will be administered to plots of coral reef underwater, (4) measurements of the capacity of coral reef organisms to change through evolutionary and induced responses to improve their resistance to OA, and (5) application of emerging theories to couple studies of individual organisms to studies of whole coral reefs. Broader impacts will accrue through a better understanding of the ways in which OA will affect coral reefs that are the poster child for demonstrating climate change effects in the marine environment, and which provide income, food, and coastal protection to millions of people living in coastal areas, including in the United States.�
This project focuses on the effects of Ocean Acidification on tropical coral reefs and builds on a program of research results from an existing 4-year award, and closely interfaces with the technical, hardware, and information infrastructure provided through the Moorea Coral Reef (MCR) LTER. The MCR-LTER, provides an unparalleled opportunity to partner with a study of OA effects on a coral reef with a location that arguably is better instrumented and studied in more ecological detail than any other coral reef in the world. Therefore, the results can be both contextualized by a high degree of ecological and physical relevance, and readily integrated into emerging theory seeking to predict the structure and function of coral reefs in warmer and more acidic future oceans. The existing award has involved a program of study in Moorea that has focused mostly on short-term organismic and ecological responses of corals and calcified algae, experiments conducted in mesocosms and flumes, and measurements of reef-scale calcification. This new award involves three new technical advances: for the first time, experiments will be conducted of year-long duration in replicate outdoor flumes; CO2 treatments will be administered to fully intact reef ecosystems in situ using replicated underwater flumes; and replicated common garden cultivation techniques will be used to explore within-species genetic variation in the response to OA conditions. Together, these tools will be used to support research on corals and calcified algae in three thematic areas: (1) tests for long-term (1 year) effects of OA on growth, performance, and fitness, (2) tests for depth-dependent effects of OA on reef communities at 20-m depth where light regimes are attenuated compared to shallow water, and (3) tests for beneficial responses to OA through intrinsic, within-species genetic variability and phenotypic plasticity. Some of the key experiments in these thematic areas will be designed to exploit integral projection models (IPMs) to couple organism with community responses, and to support the use of the metabolic theory of ecology (MTE) to address scale-dependence of OA effects on coral reef organisms and the function of the communities they build.
The following publications and data resulted from this project:
Comeau S, Carpenter RC, Lantz CA, Edmunds PJ. (2016) Parameterization of the response of calcification to temperature and pCO2 in the coral Acropora pulchra and the alga Lithophyllum kotschyanum. Coral Reefs 2016.�DOI 10.1007/s00338-016-1425-0.calcification rates�(2014)calcification rates (2010)
Comeau, S., Carpenter, R.C., Edmunds, P.J. �(2016) Effects of pCO2 on photosynthesis and respiration of tropical scleractinian corals and calcified algae. ICES Journal of Marine Science doi:10.1093/icesjms/fsv267.respiration and photosynthesis Irespiration and photosynthesis II
Evensen, N.R. & Edmunds P. J. (2016) Interactive effects of ocean acidification and neighboring corals on the growth of Pocillopora verrucosa. Marine Biology, 163:148. doi:�10.1007/s00227-016-2921-zcoral growthseawater chemistrycoral colony interactions";
    String projects_1_end_date "2018-12";
    String projects_1_geolocation "Moorea, French Polynesia";
    String projects_1_name "Collaborative Research: Ocean Acidification and Coral Reefs: Scale Dependence and Adaptive Capacity";
    String projects_1_project_nid "535322";
    String projects_1_project_website "http://mcr.lternet.edu";
    String projects_1_start_date "2015-01";
    String publisher_name "Shannon Rauch";
    String publisher_role "BCO-DMO Data Manager(s)";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v29";
    String summary "Calcification of coral from the start and end of experiments under elevated concentrations of temperature and carbon dioxide.";
    String title "Calcification of coral from the start and end of experiments under elevated concentrations of temperature and carbon dioxide";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.0-alpha";
  }
}

 

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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