Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | [Gulf of Alaska copepods: annotated transcriptomes] - Annotated de novo transcriptomes generated from six co-occurring species of calanoid copepods from the R/V Tiglax TXF18, TXS19, TXF15, TXF17 in the Gulf of Alaska from 2015- 2019 (Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_908689_v1) |
| Information: | Summary
| License
| FGDC
| ISO 19115
| Metadata
| Background
| Files
| Make a graph
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Attributes {
s {
seq_id {
String long_name "Seq_id";
String units "unitless";
}
Genbank_accession {
String long_name "Genbank_accession";
String units "unitless";
}
Species {
String long_name "Species";
String units "unitless";
}
Station {
String long_name "Station";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float32 actual_range 59.845, 60.6667;
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 -149.4667, -147.6667;
String axis "X";
String ioos_category "Location";
String long_name "Longitude";
String standard_name "longitude";
String units "degrees_east";
}
Collection_date {
String long_name "Collection_date";
String units "unitless";
}
Depth_range {
String long_name "Depth_range";
String units "meters (m)";
}
Life_stage {
String long_name "Life_stage";
String units "unitless";
}
Sex {
String long_name "Sex";
String units "unitless";
}
Entry {
String long_name "Entry";
String units "unitless";
}
Entry_name {
String long_name "Entry_name";
String units "unitless";
}
evalue {
String long_name "Evalue";
String units "unitless";
}
Protein_names {
String long_name "Protein_names";
String units "unitless";
}
Gene_names {
String long_name "Gene_names";
String units "unitless";
}
Organism {
String long_name "Organism";
String units "unitless";
}
Cross_reference_KEGG {
String long_name "Cross_reference_kegg";
String units "unitless";
}
Gene_ontology_IDs {
String long_name "Gene_ontology_ids";
String units "unitless";
}
Gene_ontology_GO {
String long_name "Gene_ontology_go";
String units "unitless";
}
Gene_ontology_biological_process {
String long_name "Gene_ontology_biological_process";
String units "unitless";
}
Gene_ontology_cellular_component {
String long_name "Gene_ontology_cellular_component";
String units "unitless";
}
Gene_ontology_molecular_function {
String long_name "Gene_ontology_molecular_function";
String units "unitless";
}
BioProject {
String long_name "Bioproject";
String units "unitless";
}
TSA_Master_Accession {
String long_name "Tsa_master_accession";
String units "unitless";
}
Study_Accession {
String long_name "Study_accession";
String units "unitless";
}
Study_Title {
String long_name "Study_title";
String units "unitless";
}
Experiement_Accession {
String long_name "Experiement_accession";
String units "unitless";
}
Experiment_Title {
String long_name "Experiment_title";
String units "unitless";
}
SRA_Accession {
String long_name "Sra_accession";
String units "unitless";
}
BioSample {
String long_name "Biosample";
String units "unitless";
}
Sample_Accession {
String long_name "Sample_accession";
String units "unitless";
}
}
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.908689.1";
Float64 Easternmost_Easting -147.6667;
Float64 geospatial_lat_max 60.6667;
Float64 geospatial_lat_min 59.845;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -147.6667;
Float64 geospatial_lon_min -149.4667;
String geospatial_lon_units "degrees_east";
String history
"2024-11-23T16:51:05Z (local files)
2024-11-23T16:51:05Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_908689_v1.html";
String infoUrl "https://www.bco-dmo.org/dataset/908689";
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 60.6667;
String sourceUrl "(local files)";
Float64 Southernmost_Northing 59.845;
String summary
"The dataset includes the annotation files of nine high-quality de novo transcriptomes generated from shotgun assemblies of short-sequence reads. The species are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. The de novo assemblies included one generated several years ago plus eight new ones generated from six co-occurring species of calanoid copepods in the Gulf of Alaska. The transcriptomes include the first published ones for Neocalanus plumchrus, Neocalanus cristatus, Eucalanus bungii and Metridia pacifica and three for Neocalanus flemingeri and two for Calanus marshallae. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Short-sequence reads were assembled with Trinity software and resulting transcripts were annotated using the SwissProt database with additional functional annotation using gene ontology terms and enzyme function. The annotations files are the first ones published for these species. The integrated dataset can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes using the annotations.
These data are further described in the following publications: Hartline, et al. (2023) (DOI: 10.1038/s41597-023-02130-1), Roncalli, et al. (2022) (DOI: 10.1111/mec.16354), and Roncalli, et al. (2019) (DOI: 10.1038/s42003-019-0565-5)";
String title "[Gulf of Alaska copepods: annotated transcriptomes] - Annotated de novo transcriptomes generated from six co-occurring species of calanoid copepods from the R/V Tiglax TXF18, TXS19, TXF15, TXF17 in the Gulf of Alaska from 2015-2019 (Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska)";
Float64 Westernmost_Easting -149.4667;
}
}
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.