Accessing BCO-DMO data
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| Dataset Title: | [Reciprocal transplant expt. - PSII of random colonies] - Photosystem II (PSII) photochemical efficiency (Yield PSII) recorded at noon (ΔF/Fm') and at dusk (Fv/Fm) on random coral colonies of Orbicella faveolata from Varadero and Rosario reefs, Colombia, May 2017 (RAPID: Coral robustness: lessons from an "improbable" reef) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_786548) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
Date {
String bcodmo_name "date";
String description "sampling date";
String long_name "Date";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String time_precision "1970-01-01";
String units "unitless";
}
time2 {
String bcodmo_name "time";
String description "sampling time";
String long_name "Time";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AHMSAA01/";
String units "unitless";
}
Type {
String bcodmo_name "sample_descrip";
String description "type of measurement: deltaF/Fm' (effective photochemical efficiency of Photosystem II measured at noon); Fv/Fm (maximum potochemical efficiency of Photosystem II measured at dusk)";
String long_name "Type";
String units "unitless";
}
Site {
String bcodmo_name "site";
String description "sampling location";
String long_name "Site";
String units "unitless";
}
Colony {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 15;
String bcodmo_name "sample";
String description "colony identifier";
String long_name "Colony";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
F {
Int16 _FillValue 32767;
Int16 actual_range 139, 350;
String bcodmo_name "Fv2Fm";
String description "minimal Chl a fluorescence yield";
String long_name "F";
String units "unitless";
}
Fm_prime {
Int16 _FillValue 32767;
Int16 actual_range 308, 950;
String bcodmo_name "Fv2Fm";
String description "maximal Chl a fluorescence yield (= Fm when measured at dusk and Fm' when measured at noon)";
String long_name "Fm Prime";
String units "unitless";
}
Yield_PSII {
Float32 _FillValue NaN;
Float32 actual_range 0.448, 0.716;
String bcodmo_name "Fv2Fm";
String description "maximum or effective photochemical efficiency of Photosystem II when measurement takes place at dusk (Fv/Fm) or at noon (?F/Fm') respectively";
String long_name "Yield PSII";
String units "unitless";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 4.6, 25.8;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "sampling depth";
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";
}
time {
String _CoordinateAxisType "Time";
Float64 actual_range 1.511976655e+9, 1.512663738e+9;
String axis "T";
String bcodmo_name "ISO_DateTime_UTC";
String description "date and time formatted is ISO: yyyy-mm-ddTHH:MM:SSZ";
String ioos_category "Time";
String long_name "ISO Date Time UTC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/";
String source_name "ISO_DateTime_UTC";
String standard_name "time";
String time_origin "01-JAN-1970 00:00:00";
String time_precision "1970-01-01T00:00:00Z";
String units "seconds since 1970-01-01T00:00:00Z";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"The Photosystem II (PSII) photochemical efficiency (Yield PSII) was recorded
at noon (\\u0394F/Fm') and at dusk (Fv/Fm) on corals from the species Orbicella
faveolata.
Measurements were recorded on corals used in a reciprocal transplant
experiment and on random colonies.\\u00a0Data from three study sites are
reported: Varadero at 3.5m depth (10\\u00b018\\u201923.3\\u201dN,
75\\u00b035\\u201908.0\\u201dW); Rosario at 12m depth (10\\u00b011'12.1\\\"N,
75\\u00b044'43.0\\\"W); and Cartagena Bay at 3m depth (10\\u00b018'5.80\\\"N,
75\\u00b034'37.10\\\"W).\\u00a0Varadero and Rosario were both source and
destination sites; Cartagena Bay was only a destination site.\\u00a0
The maximum quantum yield of PSII (Fv/Fm) was recorded at dusk and the
effective quantum yield of PSII (\\u0394F/Fm\\u2019) at local noon during peak
of sunlight exposure. Measurements were performed with a submergible Pulse
Amplitud Modulated fluorometer (diving-PAM, Walz, Germany) on fragments used
in a reciprocal transplant experiment and on colonies randomly distributed at
similar depths compared to the transplant experiment. Three study sites with
contrasting exposure to the Dique channel freshwater plume were considered: 1)
Varadero reef at 3.5m depth close to the Dique channel mouth
(10\\u00b018\\u201923.3\\u201dN, 75\\u00b035\\u201908.0\\u201dW), 2) Rosario reef at
12m depth as clear-control site located 21 km southwest of Varadero
(10\\u00b011'12.1\\\"N, 75\\u00b044'43.0\\\"W), and 3) Cartagena Bay at 3m depth,
the closest site to the Dique channel mouth (10\\u00b018'5.80\\\"N,
75\\u00b034'37.10\\\"W).
The software WinControl-3 was used to operate and download the data from the
diving-PAM.";
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
"Photosystem II (PSII) photochemical efficiency (Yield PSII) recorded at noon (deltaF/Fm') and at dusk (Fv/Fm) on corals from the species Orbicella faveolata
Random colonies from Varadero and Rosario reefs, May 2017
PI: M. Medina, R. Iglesias-Prieto, T. Lopez (Penn State)
version date: 2020-01-08";
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 "2020-01-08T19:20:02Z";
String date_modified "2020-03-04T21:25:01Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.786548.1";
Float64 geospatial_vertical_max 25.8;
Float64 geospatial_vertical_min 4.6;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-19T18:30:05Z (local files)
2024-11-19T18:30:05Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_786548.html";
String infoUrl "https://www.bco-dmo.org/dataset/786548";
String institution "BCO-DMO";
String instruments_0_acronym "Fluorometer";
String instruments_0_dataset_instrument_description "An underwater Pulse Amplitude Modulated fluorometer (diving-PAM, Walz, Germany) was used to measure the PSII photochemical efficiency.";
String instruments_0_dataset_instrument_nid "786555";
String instruments_0_description "A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/113/";
String instruments_0_instrument_name "Fluorometer";
String instruments_0_instrument_nid "484";
String instruments_0_supplied_name "diving-PAM, Walz, Germany";
String keywords "bco, bco-dmo, biological, chemical, colony, data, dataset, date, depth, dmo, erddap, Fm_prime, iso, management, oceanography, office, preliminary, prime, psii, site, time, time2, type, yield, Yield_PSII";
String license "https://www.bco-dmo.org/dataset/786548/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/786548";
String param_mapping "{'786548': {'Depth': 'master - depth', 'ISO_DateTime_UTC': 'flag - time'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/786548/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 "Photosystem II (PSII) photochemical efficiency (Yield PSII) recorded at noon (\\u0394F/Fm') and at dusk (Fv/Fm) on random coral colonies of Orbicella faveolata for a reciprocal transplant experiment, from Varadero and Rosario reefs, Colombia, May 2017";
String time_coverage_end "2017-12-07T16:22:18Z";
String time_coverage_start "2017-11-29T17:30:55Z";
String title "[Reciprocal transplant expt. - PSII of random colonies] - Photosystem II (PSII) photochemical efficiency (Yield PSII) recorded at noon (ΔF/Fm') and at dusk (Fv/Fm) on random coral colonies of Orbicella faveolata from Varadero and Rosario reefs, Colombia, May 2017 (RAPID: Coral robustness: lessons from an \"improbable\" reef)";
String version "1";
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.