http://lod.bco-dmo.org/id/dataset/536485
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2014-10-29
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Results of cluster analysis and gene ontology: carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project)
2014-10-29
publication
2014-10-29
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-05-18
publication
https://doi.org/10.26008/1912/bco-dmo.536485.1
Paul G. Falkowski
Rutgers University
principalInvestigator
Yair Rosenthal
Rutgers University
principalInvestigator
Oscar M.E. Schofield
Rutgers University
principalInvestigator
Robert M. Sherrell
Rutgers University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Falkowski, P. G., Rosenthal, Y., Schofield, O. M., Sherrell, R. M. (2022) Results of cluster analysis and gene ontology: carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2014-10-29 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.536485.1 [access date]
Carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin. Dataset Description: <p>Cluster analysis and gene ontology to compare ~1500 proteins, from over 100 studies, extracted from calcium carbonates in stony corals, bivalve and gastropod mollusks, and adult and larval sea urchins. This dataset includes information presented in Supplemental Table S2 from Drake et al. 2014. Refer to Drake et al. (2014) for more information on methodology and results.</p> Methods and Sampling: <p><em>Methodology described in Drake et al. 2014:</em><br />
Sequences from over 100 biomineral proteome studies were grouped by hierarchical clustering using the CD-HIT suite web server (Li and Godzik, 2006; Huang et al., 2010; <a href="http://weizhong-lab.ucsd.edu/cd-hit/" target="_blank">http://weizhong-lab.ucsd.edu/cd-hit/</a>) and assigned gene ontology (GO) terms using Blast2Go software (Conesa et al., 2005). Although 1531 proteins reduced to 1051 clusters at 30% similarity, only 64 clusters showed sequence similarity across phyla. Studies published from the 1990s through June 2013, using N-terminal and mass spectrometry COM sequencing, RT-PCR, or GO and KEGG annotation of genomic and transcriptomic data sets are included. Mass spectrometry sequences were excluded if the experimental data were compared with gene models from a different species.</p>
<p><em>This dataset includes information presented in Supplemental Table S2 from Drake et al. 2014:</em><br />
Proteins from coral, mollusk, and sea urchin direct COM sequencing, RT-PCR, or GO and KEGG annotation. 1076 proteins, including redundancy when noted by multiple sources, reduced to 1031 non-redundant sequences.</p>
Funding provided by NSF Emerging Frontiers Division (NSF EF) Award Number: EF-1041143 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1041143
completed
Paul G. Falkowski
Rutgers University
848-932-3426
Institute of Marine & Coastal Sciences 71 Dudley Road, Cook Campus
New Brunswick
NJ
08901
USA
falko@imcs.rutgers.edu
pointOfContact
Yair Rosenthal
Rutgers University
71 Dudley Road
New Brunswick
NJ
08901
United States
rosentha@marine.rutgers.edu
pointOfContact
Oscar M.E. Schofield
Rutgers University
732-932-6555 x548
Institute of Marine and Coastal Studies 71 Dudley Road
New Brunswick
NJ
08901-8525
USA
oscar@marine.rutgers.edu
pointOfContact
Robert M. Sherrell
Rutgers University
848-932-3403
Rutgers Inorganic Analytical Laboratory (RIAL) 71 Dudley Rd
New Brunswick
NJ
08901-8521
USA
sherrell@marine.rutgers.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
protein_name
cluster_num
group_num
genus
species
taxon
reference
ID1
detection_type
type
Mass Spec
theme
None, User defined
No BCO-DMO term
genus
species scientific name (binomial)
taxon
reference_paper
featureType
BCO-DMO Standard Parameters
Mass Spectrometer
instrument
BCO-DMO Standard Instruments
lab_Falkowski
service
Deployment Activity
New Brunswick, NJ
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA)
https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503477
Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA)
NSF Climate Research Investment (CRI) activities that were initiated in 2010 are now included under Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES). SEES is a portfolio of activities that highlights NSF's unique role in helping society address the challenge(s) of achieving sustainability. Detailed information about the SEES program is available from NSF (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504707).
In recognition of the need for basic research concerning the nature, extent and impact of ocean acidification on oceanic environments in the past, present and future, the goal of the SEES: OA program is to understand (a) the chemistry and physical chemistry of ocean acidification; (b) how ocean acidification interacts with processes at the organismal level; and (c) how the earth system history informs our understanding of the effects of ocean acidification on the present day and future ocean.
Solicitations issued under this program:
NSF 10-530, FY 2010-FY2011
NSF 12-500, FY 2012
NSF 12-600, FY 2013
NSF 13-586, FY 2014
NSF 13-586 was the final solicitation that will be released for this program.
PI Meetings:
1st U.S. Ocean Acidification PI Meeting(March 22-24, 2011, Woods Hole, MA)
2nd U.S. Ocean Acidification PI Meeting(Sept. 18-20, 2013, Washington, DC)
3rd U.S. Ocean Acidification PI Meeting (June 9-11, 2015, Woods Hole, MA – Tentative)
NSF media releases for the Ocean Acidification Program:
Press Release 10-186 NSF Awards Grants to Study Effects of Ocean Acidification
Discovery Blue Mussels "Hang On" Along Rocky Shores: For How Long?
Discovery nsf.gov - National Science Foundation (NSF) Discoveries - Trouble in Paradise: Ocean Acidification This Way Comes - US National Science Foundation (NSF)
Press Release 12-179 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: Finding New Answers Through National Science Foundation Research Grants - US National Science Foundation (NSF)
Press Release 13-102 World Oceans Month Brings Mixed News for Oysters
Press Release 13-108 nsf.gov - National Science Foundation (NSF) News - Natural Underwater Springs Show How Coral Reefs Respond to Ocean Acidification - US National Science Foundation (NSF)
Press Release 13-148 Ocean acidification: Making new discoveries through National Science Foundation research grants
Press Release 13-148 - Video nsf.gov - News - Video - NSF Ocean Sciences Division Director David Conover answers questions about ocean acidification. - US National Science Foundation (NSF)
Press Release 14-010 nsf.gov - National Science Foundation (NSF) News - Palau's coral reefs surprisingly resistant to ocean acidification - US National Science Foundation (NSF)
Press Release 14-116 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: NSF awards $11.4 million in new grants to study effects on marine ecosystems - US National Science Foundation (NSF)
SEES-OA
largerWorkCitation
program
The Molecular Basis of Ocean Acidification Effects on Calcification in Zooxanthellate Corals
http://corals.marine.rutgers.edu/
The Molecular Basis of Ocean Acidification Effects on Calcification in Zooxanthellate Corals
<p><em>From the NSF award abstract:</em></p>
<p>Ocean acidification (the decrease in seawater pH) is driven by the increase in atmospheric CO2. This is expected to have a dramatic effect on organisms that precipitate calcium carbonate. Coral reefs are formed and maintained by calcifying organisms, particularly reef-building corals. Current predictions are that coral species will be negatively impacted; however the limited number of available measurements exhibit significant variability for reasons that are not understood. This is critically important as coral reef ecosystems hold significant cultural and economic values both nationally and internationally. This program is therefore focused on the molecular basis for calcification in corals in order to understand how corals will respond to ocean acidification in the next century. Rutgers University has a state-of-art coral culture facility that will be used to simulate future ocean conditions. The work will utilize a unique set of coral tissue cultures that will allow scientists to assess the cellular biology that underlies the responses of corals to ocean acidification. The laboratory measurements will also determine how geochemical signatures of corals are affected by varying environmental conditions. These results are important because coral geochemical signatures are used to understand how corals have responded to changes in the ocean pH in the historical past. The project will be conducted by a research team at Rutgers, in collaboration with scientists in Taiwan and Israel.</p>
CROA
largerWorkCitation
project
eng; USA
biota
oceans
New Brunswick, NJ
2014-10-29
laboratory-based in New Brunswick, NJ
0
BCO-DMO catalogue of parameters from Results of cluster analysis and gene ontology: carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin; analyzed in the Falkowski lab at Rutgers from 2010-2014 (CROA project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/536496.rdf
Name: protein_name
Units: text
Description: <p>Name of the protein.</p>
http://lod.bco-dmo.org/id/dataset-parameter/536497.rdf
Name: cluster_num
Units: unitless
Description: <p>Cluster numbers were assigned to each batch of proteins that clustered together with 30% similarity or higher based on a clustering method using the CD-HIT suite web server. This was done progressively from 100% sequence similarity down to 30% with the cluster numbers carrying through. However, if a protein showed 30% similarity to another batch of proteins, then, for the final cut-off of 30%, the proteins from the previously independent batch were grouped in with the new batch. For instance, Cluster005744 has a cluster_num of 12. That means that it has 30% sequence similarity with proteins from proteins 5955, 00152 1(a), and 19987. In a previous clustering (with a higher similarity cutoff), it also showed sequence similarity with proteins Cluster020987, Cluster020227, and Cluster015890 (so they were previously in cluster #12). However, now proteins Cluster020987, Cluster020227, and Cluster015890 show at least 30% sequence similarity with one of the Cluster000783, Cluster050768, Cluster050003, or lotgi1|230171 proteins (that were previously assigned to cluster #0). So now since at least 1 protein in cluster #12 is similar to cluster #0, all #12 proteins were assigned to cluster #0.</p>
http://lod.bco-dmo.org/id/dataset-parameter/536498.rdf
Name: group_num
Units: unitless
Description: <p>Group number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/536499.rdf
Name: genus
Units: text
Description: <p>Genus name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/536500.rdf
Name: species
Units: text
Description: <p>Species name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/536501.rdf
Name: taxon
Units: text
Description: <p>Taxonomic grouping (coral, echinoderm, or mollusk).</p>
http://lod.bco-dmo.org/id/dataset-parameter/536502.rdf
Name: reference
Units: text
Description: <p>Reference paper. Refer to Supplemental Files for full citations.</p>
http://lod.bco-dmo.org/id/dataset-parameter/536503.rdf
Name: ID1
Units: text
Description: <p>The accession number, author's assigned protein number, or other note about a designator for the individual protein.</p>
http://lod.bco-dmo.org/id/dataset-parameter/536504.rdf
Name: detection_type
Units: text
Description: <p>Method used to sequence the protein.The strings of letters are the individual peptide sequences detected by LC-MS/MS.</p>
http://lod.bco-dmo.org/id/dataset-parameter/536505.rdf
Name: type
Units: text
Description: <p>Indicates if the protein can be assigned the name of a type of protein based on BLAST similarity. Also contains notes, such as if the protein was assigned its own accession number but was the same protein as found in another row.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
135096
https://darchive.mblwhoilibrary.org/bitstream/1912/28811/1/dataset-536485_cluster-analysis-carbonate-organic-matrix-proteins__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.536485.1
download
onLine
dataset
<p><em>Methodology described in Drake et al. 2014:</em><br />
Sequences from over 100 biomineral proteome studies were grouped by hierarchical clustering using the CD-HIT suite web server (Li and Godzik, 2006; Huang et al., 2010; <a href="http://weizhong-lab.ucsd.edu/cd-hit/" target="_blank">http://weizhong-lab.ucsd.edu/cd-hit/</a>) and assigned gene ontology (GO) terms using Blast2Go software (Conesa et al., 2005). Although 1531 proteins reduced to 1051 clusters at 30% similarity, only 64 clusters showed sequence similarity across phyla. Studies published from the 1990s through June 2013, using N-terminal and mass spectrometry COM sequencing, RT-PCR, or GO and KEGG annotation of genomic and transcriptomic data sets are included. Mass spectrometry sequences were excluded if the experimental data were compared with gene models from a different species.</p>
<p><em>This dataset includes information presented in Supplemental Table S2 from Drake et al. 2014:</em><br />
Proteins from coral, mollusk, and sea urchin direct COM sequencing, RT-PCR, or GO and KEGG annotation. 1076 proteins, including redundancy when noted by multiple sources, reduced to 1031 non-redundant sequences.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing Notes:<br />
- Replaced blanks with 'nd' to indicate 'no data'.<br />
- Replaced alpha symbols with the word "alpha" and beta symbols with "beta".<br />
- Created code list ("<span style="font-size:13px"><a href="https://datadocs.bco-dmo.org/docs/302/falkowski/CROA/data_docs/SI_Table_2_sequence_codes.csv" target="_blank">SI_Table_2_sequence_codes.csv</a>")</span> for long sequences contained in the 'detection_type' column.<br />
- Created reference list&nbsp;("<span style="font-size:13px"><a href="https://datadocs.bco-dmo.org/docs/302/falkowski/CROA/data_docs/SI_Table_2_references.csv" target="_blank">SI_Table_2_references.csv</a>")&nbsp;</span>for full references of names in the 'reference' column.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Mass Spec
Mass Spec
PI Supplied Instrument Name: Mass Spec Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Deployment: lab_Falkowski
lab_Falkowski
Rutgers_New_Brunswick
laboratory
lab_Falkowski
Paul G. Falkowski
Rutgers University
Rutgers_New_Brunswick
laboratory