Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | Symbiont removed and anemone reinfected with one of two strains of Symbiodinium from (AnemoneOA project) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_649728) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
sample {
String bcodmo_name "sample";
String description "Sample ID number";
String long_name "Sample";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
symbiont_id {
String bcodmo_name "taxon";
String description "Symbiont identity; i.e. Homologous ITS2-type A4 Symbiodinium or Symbiodinium minutum ITS2-type B1";
String long_name "Symbiont Id";
String units "text";
}
anemone_resp_rate {
Float64 _FillValue NaN;
Float64 actual_range 0.813157803, 2.214224466;
String bcodmo_name "O2 consumption";
String description "Host protein-normalised holobiont respiration rate";
String long_name "Anemone Resp Rate";
String units "micromoles of oxygen per hour per milligram protein";
}
host_CS_act {
Float64 _FillValue NaN;
Float64 actual_range 0.06816797, 0.185088974;
String bcodmo_name "metabolic_enzyme";
String description "Host (anemone) citrate synthase specific activity";
String long_name "Host CS Act";
String units "Units per milligram protein";
}
symbiont_CS_act {
Float64 _FillValue NaN;
Float64 actual_range 0.009343539, 0.13640119;
String bcodmo_name "metabolic_enzyme";
String description "Symbiont (Symbiodinium) citrate synthase specific activity";
String long_name "Symbiont CS Act";
String units "Units per milligram protein";
}
photo_output_symb {
Float64 _FillValue NaN;
Float64 actual_range 0.184067192, 1.337695877;
String bcodmo_name "photosynthesis";
String description "Net photosynthesis per symbiont cell";
String long_name "Photo Output Symb";
String units "picomoles oxygen per hour per cell";
}
symbio_density {
Float64 _FillValue NaN;
Float64 actual_range 1098543.993, 8812379.853;
String bcodmo_name "abundance";
String description "Host protein-normalised symbiont density";
String long_name "Symbio Density";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "million cells per mg protein";
}
symbio_biomass_fraction {
Float32 _FillValue NaN;
Float32 actual_range 0.0183, 0.1581;
String bcodmo_name "unknown";
Float64 colorBarMaximum 1.0;
Float64 colorBarMinimum 0.0;
String description "Symbiont biomass fraction (calculated as total symbiont protein [mg]/total host+symbiont protein [mg])";
String long_name "Symbio Biomass Fraction";
String units "milligrams per milligrams(dimensionless)";
}
symbio_resp_fraction {
Float32 _FillValue NaN;
Float32 actual_range 0.0041, 0.1433;
String bcodmo_name "unknown";
Float64 colorBarMaximum 1.0;
Float64 colorBarMinimum 0.0;
String description "Symbiont respiration fraction (calculated as total symbiont citrate synthase activity [U]/total host+symbiont citrate synthase activity [U])";
String long_name "Symbio Resp Fraction";
String units "dimensionless";
}
resp_biom_quotient {
Float64 _FillValue NaN;
Float64 actual_range 0.072127984, 1.036789977;
String bcodmo_name "unknown";
String description "Symbiont respiration fraction/Symbiont biomass fraction";
String long_name "Resp Biom Quotient";
String units "dimensionless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description "Full details of the experimental design are provided in Hawkins et al., 2016";
String awards_0_award_nid "628966";
String awards_0_award_number "EF-1316055";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1316055";
String awards_0_funder_name "NSF Emerging Frontiers Division";
String awards_0_funding_acronym "NSF EF";
String awards_0_funding_source_nid "392";
String awards_0_program_manager "Irwin Forseth";
String awards_0_program_manager_nid "520504";
String cdm_data_type "Other";
String comment
"Sea Anemone respiratory capacity
with two different symbionts
in an experimental setting
CS = Citrate Synthase
M. Warner, PI
Version 14 June 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 "2016-06-17T15:05:21Z";
String date_modified "2019-07-02T15:06:36Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.649728.1";
String history
"2024-04-18T22:42:12Z (local files)
2024-04-18T22:42:12Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_649728.html";
String infoUrl "https://www.bco-dmo.org/dataset/649728";
String institution "BCO-DMO";
String instruments_0_dataset_instrument_description
"[EVOS system, ThermoFisher (Life Technologies), Waltham, MA, USA; excitation: 628 ± 20 nm, emission: 692 ± 20 nm].
Field of view was determined using the EVOS operating software (4× objective), and cells were counted using the “Analyze Particles” tool in ImageJ (NIH, Bethesda, MD, USA).";
String instruments_0_dataset_instrument_nid "652568";
String instruments_0_description "Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB06/";
String instruments_0_instrument_name "Microscope-Fluorescence";
String instruments_0_instrument_nid "695";
String instruments_0_supplied_name "Fluorescence Microscope";
String instruments_1_dataset_instrument_description "an oxygen sensitive optode (Fibox 4, PreSens Gmbh, Regensburg, Germany).";
String instruments_1_dataset_instrument_nid "652570";
String instruments_1_description "An optode or optrode is an optical sensor device that optically measures a specific substance usually with the aid of a chemical transducer.";
String instruments_1_instrument_name "Optode";
String instruments_1_instrument_nid "727";
String instruments_1_supplied_name "oxygen sensitive optode";
String instruments_2_acronym "Thermal Cycler";
String instruments_2_dataset_instrument_description "AB-7500 real-time QPCR system [ThermoFisher (Applied Biosystems), Waltham, MA, USA], with the following cycling conditions: 94◦ C for 10 min, followed by 40 cycles of 94◦C for 15 s, 60◦C for 1 min, and 72◦C for 15 s.";
String instruments_2_dataset_instrument_nid "652569";
String instruments_2_description
"General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)";
String instruments_2_instrument_name "PCR Thermal Cycler";
String instruments_2_instrument_nid "471582";
String instruments_2_supplied_name "ThermoFisher QPCR system";
String keywords "act, anemone, anemone_resp_rate, bco, bco-dmo, biological, biom, biomass, chemical, data, dataset, density, dmo, erddap, fraction, host, host_CS_act, management, oceanography, office, output, photo, photo_output_symb, preliminary, quotient, rate, resp, resp_biom_quotient, sample, symb, symbio, symbio_biomass_fraction, symbio_density, symbio_resp_fraction, symbiont, symbiont_CS_act, symbiont_id";
String license "https://www.bco-dmo.org/dataset/649728/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/649728";
String param_mapping "{'649728': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/649728/parameters";
String people_0_affiliation "University of Delaware";
String people_0_person_name "Mark E. Warner";
String people_0_person_nid "51387";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI BCO-DMO";
String people_1_person_name "Ms Dicky Allison";
String people_1_person_nid "50382";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "AnemoneOA";
String projects_0_acronym "AnemoneOA";
String projects_0_description
"The projected rise in carbon dioxide (CO2) in the atmosphere is considered a primary threat to marine systems throughout the world due to both ocean acidification and rising ocean temperatures. Coral reefs are very sensitive to these projected changes in the earth's climate, with continued losses in growth as well as disruption (also known as bleaching) in the symbiotic relationship between the algae (Symbiodinium) living within a diversity of host animals, including stony corals, soft corals and sea anemones. While much information has been gleaned as to how acidification may affect stony corals, considerably less is known about the interactive effects of acidification and temperature to other symbiotic anthozoans.
To this end, this proposal will investigate the long-term impacts of elevated CO2 and temperature on the model sea anemone, Aiptasia pallida, while harboring four different genotypes of Symbiodinium. The primary goals of this project are (1) to determine the sensitivity and capacity for acclimation in molecular and physiological processes while exposed to elevated CO2 and temperature, and (2) to assess the degree to which acclimated adult animals may confer (or transfer) an imprinted physiological characteristic to the next generation of asexual offspring. A series of long-term experiments will be conducted with each animal/algal combination (holobiont) in order to collect initial (3 month) stress markers and genomic data and then follow animal response and asexual reproduction through several generations for one year. The possibility for enhanced resilience or acclimation will be measured by tracking the recovery of each holobiont, followed by repeated exposure to elevated temperature while held in high CO2. This project will tease apart fine scale mechanisms of stress, acclimation, or amelioration that may vary as a function of algal genotype and host animal response, and the degree to which environmental imprinting may pre-acclimate propagules. Project results will provide information regarding how future acidification and warming will affect cnidarian-algal symbioses, and the fundamental profile of their flexibility in stress response processes across organismal, metabolic, genomic and epigenetic scales.";
String projects_0_end_date "2016-06";
String projects_0_geolocation "Lewes, Delaware";
String projects_0_name "Ocean Acidification: Understanding the Impact of CO2 and Temperature on the Physiological, Genetic, and Epigenetic Response of a Model Sea Anemone System with Different Symbionts";
String projects_0_project_nid "628967";
String projects_0_start_date "2013-07";
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 "Symbiont removed and anemone reinfected with one of two strains of Symbiodinium from (AnemoneOA project)";
String title "Symbiont removed and anemone reinfected with one of two strains of Symbiodinium from (AnemoneOA project)";
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.