Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | [Sites and symbionts] - Symbiodinium algae in foraminifer and corals in St. John, USVI. (LTREB Long-term coral reef community dynamics in St. John, USVI: 1987-2019) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_735079) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Files
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Attributes {
s {
Name_of_Bay {
String bcodmo_name "site";
String description "Bay sampled";
String long_name "Name Of Bay";
String units "unitless";
}
Name_of_Site {
String bcodmo_name "site";
String description "Study site";
String long_name "Name Of Site";
String units "unitless";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 5.0, 14.0;
String axis "Z";
String bcodmo_name "depth";
String description "Sampling depth";
String ioos_category "Location";
String long_name "Collection Depth";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
String positive "down";
String standard_name "depth";
String units "m";
}
Host {
String bcodmo_name "species";
String description "Host species sampled";
String long_name "Host";
String units "unitless";
}
Sample_ID {
String bcodmo_name "sample";
String description "Sample ID";
String long_name "Sample ID";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
A3 {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 5, 10;
String bcodmo_name "count";
String description "Number of Symbiodinium OTUs found in each sample";
String long_name "A3";
String units "count";
}
B1 {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 12;
String bcodmo_name "count";
String description "Number of Symbiodinium OTUs found in each sample";
String long_name "B1";
String units "count";
}
C7 {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 6;
String bcodmo_name "count";
String description "Number of Symbiodinium OTUs found in each sample";
String long_name "C7";
String units "count";
}
C12 {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 9;
String bcodmo_name "count";
String description "Number of Symbiodinium OTUs found in each sample";
String long_name "C12";
String units "count";
}
C91 {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 3, 3;
String bcodmo_name "count";
String description "Number of Symbiodinium OTUs found in each sample";
String long_name "C91";
String units "count";
}
D1a {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 12;
String bcodmo_name "count";
String description "Number of Symbiodinium OTUs found in each sample";
String long_name "D1a";
String units "count";
}
D2 {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 2, 5;
String bcodmo_name "count";
String description "Number of Symbiodinium OTUs found in each sample";
String long_name "D2";
String units "count";
}
G3_3 {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 1;
String bcodmo_name "count";
String description "Number of Symbiodinium OTUs found in each sample";
String long_name "G3 3";
String units "count";
}
G3_4 {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 2, 2;
String bcodmo_name "count";
String description "Number of Symbiodinium OTUs found in each sample";
String long_name "G3 4";
String units "count";
}
F4_8 {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 10, 10;
String bcodmo_name "count";
String description "Number of Symbiodinium OTUs found in each sample";
String long_name "F4 8";
String units "count";
}
F5_1 {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 10, 11;
String bcodmo_name "count";
String description "Number of Symbiodinium OTUs found in each sample";
String long_name "F5 1";
String units "count";
}
H1 {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 10, 10;
String bcodmo_name "count";
String description "Number of Symbiodinium OTUs found in each sample";
String long_name "H1";
String units "count";
}
H5 {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 7, 10;
String bcodmo_name "count";
String description "Number of Symbiodinium OTUs found in each sample";
String long_name "H5";
String units "count";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description "Methodology in paper: (Pochon et al., 2014)";
String awards_0_award_nid "55191";
String awards_0_award_number "DEB-0841441";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0841441&HistoricalAwards=false";
String awards_0_funder_name "National Science Foundation";
String awards_0_funding_acronym "NSF";
String awards_0_funding_source_nid "350";
String awards_0_program_manager "Saran Twombly";
String awards_0_program_manager_nid "51702";
String awards_1_award_nid "562593";
String awards_1_award_number "DEB-1350146";
String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1350146";
String awards_1_funder_name "NSF Division of Environmental Biology";
String awards_1_funding_acronym "NSF DEB";
String awards_1_funding_source_nid "550432";
String awards_1_program_manager "Betsy Von Holle";
String awards_1_program_manager_nid "701685";
String cdm_data_type "Other";
String comment
"Sites and Symbionts
P. Edmunds, PI
Version 14 September 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 version 2.3 19 Dec 2019";
String date_created "2018-05-04T19:08:24Z";
String date_modified "2019-03-25T17:53:44Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.735079.1";
Float64 geospatial_vertical_max 14.0;
Float64 geospatial_vertical_min 5.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-12-03T17:24:17Z (local files)
2024-12-03T17:24:17Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_735079.html";
String infoUrl "https://www.bco-dmo.org/dataset/735079";
String institution "BCO-DMO";
String keywords "bay, bco, bco-dmo, biological, c12, c91, chemical, collection, Collection_Depth, d1a, data, dataset, depth, dmo, erddap, F4_8, F5_1, G3_3, G3_4, host, management, name, Name_of_Bay, Name_of_Site, oceanography, office, preliminary, sample, Sample_ID, site";
String license "https://www.bco-dmo.org/dataset/735079/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/735079";
String param_mapping "{'735079': {'Collection_Depth': 'master - depth'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/735079/parameters";
String people_0_affiliation "California State University Northridge";
String people_0_affiliation_acronym "CSU-Northridge";
String people_0_person_name "Peter J. Edmunds";
String people_0_person_nid "51536";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "The Cawthron Institute";
String people_1_person_name "Xavier Pochon";
String people_1_person_nid "746205";
String people_1_role "Contact";
String people_1_role_type "related";
String people_2_affiliation "Woods Hole Oceanographic Institution";
String people_2_affiliation_acronym "WHOI BCO-DMO";
String people_2_person_name "Hannah Ake";
String people_2_person_nid "650173";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "St. John LTREB,RUI-LTREB";
String projects_0_acronym "St. John LTREB";
String projects_0_description
"Long Term Research in Environmental Biology (LTREB) in US Virgin Islands:
From the NSF award abstract:
In an era of growing human pressures on natural resources, there is a critical need to understand how major ecosystems will respond, the extent to which resource management can lessen the implications of these responses, and the likely state of these ecosystems in the future. Time-series analyses of community structure provide a vital tool in meeting these needs and promise a profound understanding of community change. This study focuses on coral reef ecosystems; an existing time-series analysis of the coral community structure on the reefs of St. John, US Virgin Islands, will be expanded to 27 years of continuous data in annual increments. Expansion of the core time-series data will be used to address five questions: (1) To what extent is the ecology at a small spatial scale (1-2 km) representative of regional scale events (10's of km)? (2) What are the effects of declining coral cover in modifying the genetic population structure of the coral host and its algal symbionts? (3) What are the roles of pre- versus post-settlement events in determining the population dynamics of small corals? (4) What role do physical forcing agents (other than temperature) play in driving the population dynamics of juvenile corals? and (5) How are populations of other, non-coral invertebrates responding to decadal-scale declines in coral cover? Ecological methods identical to those used over the last two decades will be supplemented by molecular genetic tools to understand the extent to which declining coral cover is affecting the genetic diversity of the corals remaining. An information management program will be implemented to create broad access by the scientific community to the entire data set.
The importance of this study lies in the extreme longevity of the data describing coral reefs in a unique ecological context, and the immense potential that these data possess for understanding both the patterns of comprehensive community change (i.e., involving corals, other invertebrates, and genetic diversity), and the processes driving them. Importantly, as this project is closely integrated with resource management within the VI National Park, as well as larger efforts to study coral reefs in the US through the NSF Moorea Coral Reef LTER, it has a strong potential to have scientific and management implications that extend further than the location of the study.
The following publications and data resulted from this project:
2015 Edmunds PJ, Tsounis G, Lasker HR (2015) Differential distribution of octocorals and scleractinians around St. John and St. Thomas, US Virgin Islands. Hydrobiologia. doi: 10.1007/s10750-015-2555-zoctocoral - sp. abundance and distributionDownload complete data for this publication (Excel file)
2015 Lenz EA, Bramanti L, Lasker HR, Edmunds PJ. Long-term variation of octocoral populations in St. John, US Virgin Islands. Coral Reefs DOI 10.1007/s00338-015-1315-xoctocoral survey - densitiesoctocoral counts - photoquadrats vs. insitu surveyoctocoral literature reviewDownload complete data for this publication (Excel file)
2015 Privitera-Johnson, K., et al., Density-associated recruitment in octocoral communities in St. John, US Virgin Islands, J.Exp. Mar. Biol. Ecol. DOI 10.1016/j.jembe.2015.08.006octocoral recruitmentDownload complete data for this publication (Excel file)
2014 Edmunds PJ. Landscape-scale variation in coral reef community structure in the United States Virgin Islands. Marine Ecology Progress Series 509: 137–152. DOI 10.3354/meps10891.
Data at MCR-VINP.
Download complete data for this publication (Excel file)
2014 Edmunds PJ, Nozawa Y, Villanueva RD. Refuges modulate coral recruitment in the Caribbean and Pacific. Journal of Experimental Marine Biology and Ecology 454: 78-84. DOI: 10.1016/j.jembe.2014.02.00
Data at MCR-VINP.Download complete data for this publication (Excel file)
2014 Edmunds PJ, Gray SC. The effects of storms, heavy rain, and sedimentation on the shallow coral reefs of St. John, US Virgin Islands. Hydrobiologia 734(1):143-148.
Data at MCR-VINP.Download complete data for this publication (Excel file)
2014 Levitan, D, Edmunds PJ, Levitan K. What makes a species common? No evidence of density-dependent recruitment or mortality of the sea urchin Diadema antillarum after the 1983-1984 mass mortality. Oecologia. DOI 10.1007/s00442-013-2871-9.
Data at MCR-VINP.Download complete data for this publication (Excel file)
2014 Lenz EA, Brown D, Didden C, Arnold A, Edmunds PJ. The distribution of hermit crabs and their gastropod shells on shallow reefs in St. John, US Virgin Islands. Bulletin of Marine Science 90(2):681-692. https://dx.doi.org/10.5343/bms.2013.1049
Data at MCR-VINP.Download complete data for this publication (Excel file)
2013 Edmunds PJ. Decadal-scale changes in the community structure of coral reefs in St. John, US Virgin Islands. Marine Ecology Progress Series 489: 107-123.
Data at MCR-VINP.Download complete data for this publication (zipped Excel files)
2013 Brown D, Edmunds PJ. Long-term changes in the population dynamics of the Caribbean hydrocoral Millepora spp. J. Exp Mar Biol Ecol 441: 62-70. doi: 10.1016/j.jembe.2013.01.013Millepora colony sizeMillepora cover - temps - storms 1992-2008Millepora cover 1992-2008seawater temperature USVI 1992-2008storms USVI 1992-2008Download complete data for this publication (Excel file)
2012 Brown D, Edmunds PJ. The hermit crab Calcinus tibicen lives commensally on Millepora spp. in St. John, United States Virgin Islands. Coral Reefs 32: 127-135. doi: 10.1007/s00338-012-0948-2crab abundance and coral sizecrab displacement behaviorcrab nocturnal surveyscrab predator avoidanceDownload complete data for this publication (Excel file)
2011 Green DH, Edmunds PJ. Spatio-temporal variability of coral recruitment on shallow reefs in St. John, US Virgin Islands. Journal of Experimenal Marine Biology and Ecology 397: 220-229.
Data at MCR-VINP.Download complete data for this publication (Excel file)
2011 Colvard NB, Edmunds PJ. (2011) Decadal-scale changes in invertebrate abundances on a Caribbean coral reef. Journal of Experimental Marine Biology and Ecology. 397(2): 153-160. doi: 10.1016/j.jembe.2010.11.015benthic invert codesinverts - Tektite and Yawzi Ptinverts - pooledDownload complete data for this publication (Excel file)";
String projects_0_end_date "2014-04";
String projects_0_geolocation "St. John, U.S. Virgin Islands; California State University Northridge";
String projects_0_name "LTREB Long-term coral reef community dynamics in St. John, USVI: 1987-2019";
String projects_0_project_nid "2272";
String projects_0_project_website "http://coralreefs.csun.edu/";
String projects_0_start_date "2009-05";
String projects_1_acronym "RUI-LTREB";
String projects_1_description
"Describing how ecosystems like coral reefs are changing is at the forefront of efforts to evaluate the biological consequences of global climate change and ocean acidification. Coral reefs have become the poster child of these efforts. Amid concern that they could become ecologically extinct within a century, describing what has been lost, what is left, and what is at risk, is of paramount importance. This project exploits an unrivalled legacy of information beginning in 1987 to evaluate the form in which reefs will persist, and the extent to which they will be able to resist further onslaughts of environmental challenges. This long-term project continues a 27-year study of Caribbean coral reefs. The diverse data collected will allow the investigators to determine the roles of local and global disturbances in reef degradation. The data will also reveal the structure and function of reefs in a future with more human disturbances, when corals may no longer dominate tropical reefs.
The broad societal impacts of this project include advancing understanding of an ecosystem that has long been held emblematic of the beauty, diversity, and delicacy of the biological world. Proposed research will expose new generations of undergraduate and graduate students to natural history and the quantitative assessment of the ways in which our planet is changing. This training will lead to a more profound understanding of contemporary ecology at the same time that it promotes excellence in STEM careers and supports technology infrastructure in the United States. Partnerships will be established between universities and high schools to bring university faculty and students in contact with k-12 educators and their students, allow teachers to carry out research in inspiring coral reef locations, and motivate children to pursue STEM careers. Open access to decades of legacy data will stimulate further research and teaching.";
String projects_1_end_date "2019-04";
String projects_1_geolocation "USVI";
String projects_1_name "RUI-LTREB Renewal: Three decades of coral reef community dynamics in St. John, USVI: 2014-2019";
String projects_1_project_nid "734983";
String projects_1_project_website "http://coralreefs.csun.edu/";
String projects_1_start_date "2014-05";
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 "Symbiodinium algae in foraminifer and corals in St. John, USVI.";
String title "[Sites and symbionts] - Symbiodinium algae in foraminifer and corals in St. John, USVI. (LTREB Long-term coral reef community dynamics in St. John, USVI: 1987-2019)";
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.