Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | [Whole Genome Sequencing of Eelgrass Bodega and Tomales Bay] - Sample collection information and sequence accessions at the National Center for Biotechnology Information (NCBI) for whole genome sequencing of eelgrass (Zostera marina) collected at Bodega and Tomales Bay, CA, USA from July to September 2019 (Using genomics to link traits to ecosystem function in the eelgrass Zostera marina) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_924786_v1) |
| Information: | Summary
| License
| FGDC
| ISO 19115
| Metadata
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Attributes {
s {
accession {
String long_name "Accession";
String units "unitless";
}
sample_name {
String long_name "Sample_name";
String units "unitless";
}
bioproject_accession {
String long_name "Bioproject_accession";
String units "unitless";
}
Site {
String long_name "Site";
String units "unitless";
}
organism {
String long_name "Organism";
String units "unitless";
}
collection_date {
String long_name "Collection_date";
String units "unitless";
}
isolation_source {
String long_name "Isolation_source";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float32 actual_range 38.10505, 38.33343;
String axis "Y";
String ioos_category "Location";
String long_name "Latitude";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float32 actual_range -123.0595, -122.8464;
String axis "X";
String ioos_category "Location";
String long_name "Longitude";
String standard_name "longitude";
String units "degrees_east";
}
}
NC_GLOBAL {
String cdm_data_type "Other";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_url "https://www.bco-dmo.org/";
String doi "10.26008/1912/bco-dmo.924786.1";
Float64 Easternmost_Easting -122.8464;
Float64 geospatial_lat_max 38.33343;
Float64 geospatial_lat_min 38.10505;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -122.8464;
Float64 geospatial_lon_min -123.0595;
String geospatial_lon_units "degrees_east";
String history
"2024-11-23T17:05:30Z (local files)
2024-11-23T17:05:30Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_924786_v1.html";
String infoUrl "https://www.bco-dmo.org/dataset/924786";
String institution "BCO-DMO";
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.";
Float64 Northernmost_Northing 38.33343;
String sourceUrl "(local files)";
Float64 Southernmost_Northing 38.10505;
String summary
"This dataset includes sample collection information and sequence accessions at the National Center for Biotechnology Information (NCBI) for whole genome sequencing of eelgrass (Zostera marina) collected at Bodega and Tomales Bay, California, USA from July and September of 2019. Sequence Read Archive (SRA) Experiments and BioSamples can be accessed from the NCBI BioProject PRJNA887384 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA887384/).
Results summary as described in Scheibelhut, et al. (2023): We examine genomic signals of selection in the eelgrass Zostera marina across temperature gradients in adjacent embayments. Although we find many genomic regions with signals of selection within each bay there is very little overlap in signals of selection at the SNP level, despite most polymorphisms being shared across bays. We do find overlap at the gene level, potentially suggesting multiple mutational pathways to the same phenotype. Using polygenic models we find that some sets of candidate SNPs are able to predict temperature across both bays, suggesting that small but parallel shifts in allele frequencies may be missed by independent genome scans. Together, these results highlight the continuous rather than binary nature of parallel evolution in polygenic traits and the complexity of evolutionary predictability.";
String title "[Whole Genome Sequencing of Eelgrass Bodega and Tomales Bay] - Sample collection information and sequence accessions at the National Center for Biotechnology Information (NCBI) for whole genome sequencing of eelgrass (Zostera marina) collected at Bodega and Tomales Bay, CA, USA from July to September 2019 (Using genomics to link traits to ecosystem function in the eelgrass Zostera marina)";
Float64 Westernmost_Easting -123.0595;
}
}
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.