Accessing BCO-DMO data
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| Dataset Title: | [Inferno vent plume proteins-Av1] - Proteins identified from the black smoker chimney Inferno hydrothermal vent plume meta-proteome - replicate Av1 - on the Axial seamount off the coast of Washington in 2011. (Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_627835) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
entry {
String bcodmo_name "sample";
String description "data entry number; each entry number is a unit and all columns of information with the same entry number should be considered together";
String long_name "Entry";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "number";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 45.934, 45.934;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "latitude of sample collection";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -130.0138, -130.0138;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "longitude of sample collection; West is negative";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees_east";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 1450.0, 1450.0;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "depth of sample collection";
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";
}
NCBI_FASTA_link {
String bcodmo_name "external_link";
String description "FASTA header with embedded NCBI reference number; link is to protein page in that database; several entries with multiple links separated by commas had to be put on separate lines to enable multiple links";
String long_name "NCBI FASTA Link";
String units "link";
}
protein_probability {
Float32 _FillValue NaN;
Float32 actual_range 0.9052, 1.0;
String bcodmo_name "unknown";
String description "the probability that the protein identified from the peptide sequences is correct. Only proteins identified by peptides with a protein probability of >0.9 are listed";
String long_name "Protein Probability";
String units "decimal number";
}
num_unique_peptide {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 20;
String bcodmo_name "unknown";
String description "the number of unique peptide sequences identified; unique peptide is defined as a peptide -- irrespective of its length -- that exists only in one protein of a proteome of interest. The peptide sequences themselves are in the peptide sequence column";
String long_name "Num Unique Peptide";
String units "number";
}
indep_spectra_tot {
Int16 _FillValue 32767;
Int16 actual_range 1, 218;
String bcodmo_name "unknown";
String description "number of identifying peaks from the tandem mass spectrometer";
String long_name "Indep Spectra Tot";
String units "number";
}
peptide_seq {
String bcodmo_name "unknown";
String description "amino acids identified in the peptide; A=Alanine; G=Glycine; etc";
String long_name "Peptide Seq";
String units "text";
}
consensus_annotation {
String bcodmo_name "unknown";
String description "describing protein X in terms of topic Y; these dominant active bacterial groups are determined by consensus annotation of identified proteins";
String long_name "Consensus Annotation";
String units "text";
}
KEGG_category {
String bcodmo_name "unknown";
String description "Kyoto Encyclopedia of Genes and Genomes; used to identify dominant functional classifications like metabolism or genetic information processing";
String long_name "KEGG Category";
String units "text";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Seawater (~180 L) was collected from the stable hydrothermal vent plume
issuing from the black smoker chimney Inferno (CTD17, 1 450 m). Whole water
was transferred to clean 50 L polystyrene reservoirs and concentrated to ~230
ml with a Pellicon 2 tangential flow filtration system equipped with a 30 kDa
Biomax Polyethersulfone cassette (Millipore Corporation, Billerica, MA) as
described previously (Morris et al 2010). Cells were collected and
concentrated in approximately 2 hours. Concentrated cells were flash frozen in
liquid nitrogen and stored at -80 \\u00baC until further processing at the
University of Washington.Cell counts before and after filtration (6.9 x 1010
and 2.9 x 1010, respectively) indicate that we recovered 42% of the cells
present in 180 L of hydrothermal vent plume water. Cells in the concentrated
sample were divided into replicate samples (Av1 and Av2, ~115 ml each) and
harvested by centrifuging at 4\\u00b0C for 60 min (17,000 x g). The supernatant
was discarded and cell pellets were rinsed with 100 uL of 20 mM Tris buffer pH
7.4 and stored -80\\u00b0C.
Cells were lysed using a titanium sonicating micro-probe (20 sec, 10
repetitions) in a 6M urea and 50 \\u03bcM ammonium bicarbonate solution.
Disulfide bonds were reduced with dithiothreitol and alkylated with iodo-
acetic acid. After additions of ammonium bicarbonate and methanol, 2 \\u03bcg
of sequence grade trypsin (Promega, Madison, WI) were added to each sample.
Enzymatic digestions were incubated for 12 h at 37 oC. Resulting peptides were
desalted using a macro-spin C18 column (NestGroup) following the manufacturers
guidelines prior to analysis by mass spectrometry (MS).
Peptide concentrations from Axial volcano hydrothermal vent plume proteome
replicates Av1 and Av2 were measured using the Thermo Scientific Nanodrop
2000/2000c, which measures the peptide bond absorbance at wavelength of 205
nm. Approximately 1 \\u03bcg of peptide digest was used for each injection into
the mass spectrometer. Each sample consisted of a complex mixture of peptides
that were introduced into the mass spectrometer by reverse-phase
chromatography using a brand new 15 cm long, 75 \\u03bcm i.d. fused silica
capillary column packed with C18 particles (Magic C18AQ, 100 \\u00c5, 5
\\u03bcm; Michrom, Bioresources, Inc., CA) fitted with a 2 cm long, 100 \\u03bcm
i.d. pre-column (Magic C18AQ, 200 \\u00c5, 5\\u03bcm; Michrom). Peptides were
first trapped on the pre-column (5% ACN; 4 ml min-1; 7 min). Chromatographic
separations were performed using an acidified (formic acid, 0.1% v/v) water-
acetonitrile gradient (5-35% acetonitrile in 60 min) with a total run-time of
95 minutes.
Mass spectrometry was performed on replicates Av1 and Av2 independently using
the Thermo Fisher (San Jose, Ca) linear ion trap \\u2013Orbitrap (LTQ-OT)
hybrid tandem mass spectrometer. Peptides were analyzed using the data-
independent Precursor Acquisition Independent from Ion Count (PAcIFIC) method
(Panchaud et al 2009). Rather than requiring the mass spectrometer to select
ions for fragmentation based on MS1 data, the PAcIFIC method systematically
fragments ions at all m/z channels (Panchaud et al 2011). Each method file
includes the full 95 minute linear HPLC gradient of 5-35% ACN over 60 minutes
(see above) and covers a 21.5 m/z range using 14 contiguous, unique channels
that span 2.5 m/z in the mass spectrometer. This results in a total of 45
method files per PAcIFIC analytical cycle to cover a full m/z range of
400-1400.";
String awards_0_award_nid "529021";
String awards_0_award_number "OCE-1232840";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1232840";
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 "David L. Garrison";
String awards_0_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Inferno Plume Proteins
replicate Av1
(Supplementary Table 3)
only protein probability > .9 reported
location and depth added by DMO
R.Morris, PI";
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 "2015-11-25T16:24:25Z";
String date_modified "2017-11-12T19:58:17Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.643630";
Float64 Easternmost_Easting -130.0138;
Float64 geospatial_lat_max 45.934;
Float64 geospatial_lat_min 45.934;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -130.0138;
Float64 geospatial_lon_min -130.0138;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 1450.0;
Float64 geospatial_vertical_min 1450.0;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-21T08:50:01Z (local files)
2024-11-21T08:50:01Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_627835.html";
String infoUrl "https://www.bco-dmo.org/dataset/627835";
String institution "BCO-DMO";
String instruments_0_acronym "CTD SBE 9";
String instruments_0_dataset_instrument_description "Seabird 9plus CTD with temperature and conductivity sensors.";
String instruments_0_dataset_instrument_nid "637597";
String instruments_0_description "The Sea-Bird SBE 9 is a type of CTD instrument package. The SBE 9 is the Underwater Unit and is most often combined with the SBE 11 Deck Unit (for real-time readout using conductive wire) when deployed from a research vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorometer, altimeter, etc.). Note that in most cases, it is more accurate to specify SBE 911 than SBE 9 since it is likely a SBE 11 deck unit was used. more information from Sea-Bird Electronics";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/130/";
String instruments_0_instrument_name "CTD Sea-Bird 9";
String instruments_0_instrument_nid "488";
String instruments_0_supplied_name "CTD Seabird 9 plus";
String instruments_1_acronym "Mass Spec";
String instruments_1_dataset_instrument_description
"\"The hybrid Fourier Transform (FT) mass spectrometer(MS) combines a linear ion trap
MS and the Orbitrap mass analyzer. Ions generated by API
are collected in the LTQ XL followed by axial ejection to the
C-shaped storage trap which is used to store and collisionally
cool ions before injection into the orbital trap. The ions
transferred from the C-Trap are captured in the orbital trap
by rapidly increasing the electric field and the detection of
the image current from coherent ion packets takes place
after the voltages have stabilized. Signals from each of the
orbital trap outer electrodes are amplified and transformed
into a frequency spectrum by fast Fourier transformation
which is finally converted into a mass spectrum.\" (From Fisher Scientific)";
String instruments_1_dataset_instrument_nid "627987";
String instruments_1_description "General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB16/";
String instruments_1_instrument_name "Mass Spectrometer";
String instruments_1_instrument_nid "685";
String instruments_1_supplied_name "Thermo Fisher (San Jose, Ca) linear ion trap –Orbitrap (LTQ-OT) hybrid tandem mass spectrometer";
String instruments_2_acronym "Spectrophotometer";
String instruments_2_dataset_instrument_description "Measured peptide bond absorbance at wavelength 205nm";
String instruments_2_dataset_instrument_nid "637598";
String instruments_2_description "An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.";
String instruments_2_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB20/";
String instruments_2_instrument_name "Spectrophotometer";
String instruments_2_instrument_nid "707";
String instruments_2_supplied_name "Thermo Scientific Nanodrop 2000/2000c Spectrophotometer";
String keywords "annotation, bco, bco-dmo, biological, category, chemical, consensus, consensus_annotation, data, dataset, depth, dmo, entry, erddap, fasta, indep, indep_spectra_tot, kegg, KEGG_category, latitude, link, longitude, management, ncbi, NCBI_FASTA_link, num, num_unique_peptide, oceanography, office, peptide, peptide_seq, preliminary, probability, protein, protein_probability, seq, spectra, tot, unique";
String license "https://www.bco-dmo.org/dataset/627835/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/627835";
Float64 Northernmost_Northing 45.934;
String param_mapping "{'627835': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/627835/parameters";
String people_0_affiliation "University of Washington";
String people_0_affiliation_acronym "UW";
String people_0_person_name "Robert Morris";
String people_0_person_nid "51295";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of Washington";
String people_1_affiliation_acronym "UW";
String people_1_person_name "Robert Morris";
String people_1_person_nid "51295";
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 "Ms Dicky Allison";
String people_2_person_nid "50382";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "Sulfur Oxidizers";
String projects_0_acronym "Sulfur Oxidizers";
String projects_0_description
"Description from NSF award abstract:
The ocean serves an immense reservoir of carbon, nitrogen, phosphorus, sulfur, and other elements required for all life. The active and diverse microbial populations that inhabit the oceans are responsible for mediating nutrient transformations that maintain the chemistry of seawater. A recent study identified a ubiquitous group of marine bacteria from the Arctic96BD-19 gamma-proteobacterial sulfur oxidizer (GSO) lineage that is closely related to known sulfur oxidizing species that fix inorganic carbon and oxidize sulfide in low-oxygen waters. The potential for GSOs to use reduced forms of sulfur in oxygenated waters suggests that they are a keystone species that link the marine carbon and sulfur cycles. The only known isolates from the Arctic96BD-19 lineage of GSOs are now in culture, allowing fundamental questions about their roles in carbon and sulfur cycling to be investigated. Preliminary data suggest that they use energy from the oxidation of sulfur to assimilate carbon. This project seek to address the overarching hypothesis that sulfur transformations provide the Arctic96BD- 19 lineage of GSOs with energy for organic and inorganic carbon cycling throughout the water column.
Three specific hypotheses will be tested.
1. Arctic96BD-19 cells assimilate either organic carbon or fixes inorganic carbon, depending on environmental conditions.
2. Arctic96BD-19 cells oxidize thiosulfate via formation of a tetrathionate intermediate, or using the branched thiosulfate oxidation pathway.
3. Arctic96BD-19 cells are ubiquitous sulfur oxidizers that assimilate organic and inorganic carbon through the Pacific Northwest.
A combination of laboratory growth studies of the investigator's pure cultures and comparative genomic analyses will be used. The genomic data will be used to determine whether the Arctic96BD-19 cultures possess the genetic potential to oxidize reduced sulfur to sulfate (based on possession of known core and ancillary sulfur oxidation genes), which potential oxidation pathways are used, and whether they can fix inorganic carbon. These data will help guide the physiology studies by determining the most likely forms of inorganic and organic compounds that can be utilized.
Marine bacteria are critical players in global nutrient cycles, but many of their individual and community functions in the ecosystem are not well understood. Future oceanographers will need to use cultivation-dependent and cultivation-independent methods to identify metabolic process that shape microbial communities and impact biogeochemical cycles. Student education, scientific advancement, and public awareness are all important components of this project.";
String projects_0_end_date "2015-09";
String projects_0_geolocation "North Pacific Ocean";
String projects_0_name "Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade";
String projects_0_project_nid "529022";
String projects_0_project_website "http://morrislab.ocean.washington.edu/";
String projects_0_start_date "2012-10";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 45.934;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "latitude,longitude,depth";
String summary
"Proteins identified in the Inferno hydrothermal vent plume meta-proteome
(replicate Av1).\\u00a0 Only proteins identified by peptides with a protein
probability >0.9 are listed.\\u00a0
These data are reported as Supplementary Table 3 and discussed in [Mattes et
al., 2013](\\\\http://dmoserv3.bco-
dmo.org/data_docs/SulfurOxidizers/Mattes_2013_PlumeProt.pdf\\\\).
(doi:10.1038/ismej.2013.113)
The FASTA information in the data was expanded to include the metadata when
those FASTA headers were linked to GenBank.\\u00a0
Proteins that were identified in biological replicate Av2 that were not
identified in biological replicate Av1. (GSO: Gamma Sulfur Oxidizer)
\\u00a0
\\u00a0
\\u00a0
\\u00a0
\\u00a0
\\Although fewer proteins were identified in Av2, nearly all (94%) of the
proteins identified in Av2 were also identified in Av1.\\u00a0 Differences in
the total number of proteins identified in replicate samples may result from
differences in the amount of biomass obtained during sample processing.\\
DMO notes:
Put multiple FASTA entries on separate lines
Split out one number in FASTA header for linking
Left it sorted by Total Independent Spectra column
Added linkage column
Removed commas in 'consensus annotation' column (signals database to put in
new column)
Reordered columns to put KEGG last -- much longer than any other column";
String title "[Inferno vent plume proteins-Av1] - Proteins identified from the black smoker chimney Inferno hydrothermal vent plume meta-proteome - replicate Av1 - on the Axial seamount off the coast of Washington in 2011. (Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade)";
String version "1";
Float64 Westernmost_Easting -130.0138;
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.