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  • 1
    Publication Date: 2022-05-25
    Description: Presented at AGU Fall Meeting, American Geophysical Union, Washington, D.C., 10 – 14 Dec 2018
    Description: Data repositories often transform submissions to improve understanding and reuse of data by researchers other than the original submitter. However, scientific workflows built by the data submitters often depend on the original data format. In some cases, this makes the repository’s final data product less useful to the submitter. As a result, these two workable but different versions of the data provide value to two disparate, non-interoperable research communities around what should be a single dataset. Data repositories could bridge these two communities by exposing provenance explaining the transform from original submission to final product. A subsequent benefit of this provenance would be the transparent value-add of domain repository data curation. To improve its data management process efficiency, the Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification defined by the Frictionless Data project (https://frictionlessdata.io). Recently, BCO-DMO has been using the Frictionless Data Package Pipelines Python library (https://github.com/frictionlessdata/datapackage-pipelines) to capture the data curation processing steps that transform original submissions to final data products. Because these processing steps are stored using a declarative language they can be converted to a structured provenance record using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). PROV-O abstracts the Frictionless Data elements of BCO-DMO’s workflow for capturing necessary curation provenance and enables interoperability with other external provenance sources and tools. Users who are familiar with PROV-O or the Frictionless Data Pipelines can use either record to reproduce the final data product in a machine-actionable way. While there may still be some curation steps that cannot be easily automated, this process is a step towards end-to-end reproducible transforms throughout the data curation process. In this presentation, BCO-DMO will demonstrate how Frictionless Data Package Pipelines can be used to capture data curation provenance from original submission to final data product exposing the concrete value-add of domain-specific repositories.
    Description: NSF #1435578
    Keywords: Provenance ; Frictionless Data ; Data management
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 2
    Publication Date: 2022-10-21
    Description: Presented at AGU Fall Meeting 10 – 14 December 2018, Washington, D.C.
    Description: The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a publicly accessible earth science data repository created to curate, publicly serve (publish), and archive digital data and information from biological, chemical and biogeochemical research conducted in coastal, marine, great lakes and laboratory environments. The BCO-DMO repository works closely with investigators funded through the NSF OCE Division’s Biological and Chemical Sections and Antarctic Organisms & Ecosystems. The office provides services that span the full data life cycle, from data management planning support and DOI creation, to archiving with appropriate national facilities. Recently, more and more of the projects submitted to BCO-DMO represent modeling efforts which further increase our knowledge of the chemical and biological properties within the ocean ecosystem. But, as a repository traditionally focused on observational data as a primary research output, what roles should domain-specific data repositories play in this field? Recognizing code as a first class research product, how should repositories support the discovery, access and reuse of code and software used in hypothesis driven research? We feel the time is at hand for the community to begin a concerted and holistic approach to the curation of code and software. Such strategy development should begin with asking what is the appropriate output to curate? What is the minimum metadata required for re-use? How should code be stored and accessed? Should repositories support or facilitate peer reviewing code? The answers to these questions will better inform domain-specific repositories on how to better manage code as a first class research asset in order to support the scientific community. This presentation will explore these topics, inviting discussion from the audience to advance a collective strategy.
    Description: NSF #1435578
    Keywords: Data management ; Provenance ; Data repository ; Worfklow ; Modeling Conference Name: AGU 2018 Conference Location: Washington, D.C
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 3
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publication Date: 2022-10-31
    Description: Dataset: CICLOPS Dissolved Nutrients
    Description: This dataset provides seawater macronutrient concentrations from the Amundsen and Ross Seas, including from Terra Nova Bay, collected onboard the R/V Nathaniel B. Palmer as part of the Cobalamin and Iron Co-Limitation of Phytoplankton Species (CICLOPS) expedition from December 11, 2017 to March 3, 2018. Samples analyzed for phosphate, nitrite, nitrate + nitrite, silicate and ammonia were collected from full depth profiles via a trace-metal-clean rosette (TMR), filtered with a 0.2 um filter, and stored frozen until analysis via a nutrient autoanalyzer. Sensor hydrography data from each sample depth is also provided. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/874841
    Description: NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) OPP-1644073, NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) OPP-1643684, NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) OPP-1643845
    Keywords: Ross Sea ; Amundsen Sea ; CICLOPS ; Nutrients
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 4
    Publication Date: 2022-05-26
    Description: Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 116 (2011): C12019, doi:10.1029/2010JC006553.
    Description: The Ross Sea polynya is among the most productive regions in the Southern Ocean and may constitute a significant oceanic CO2 sink. Based on results from several field studies, this region has been considered seasonally iron limited, whereby a “winter reserve” of dissolved iron (dFe) is progressively depleted during the growing season to low concentrations (~0.1 nM) that limit phytoplankton growth in the austral summer (December–February). Here we report new iron data for the Ross Sea polynya during austral summer 2005–2006 (27 December–22 January) and the following austral spring 2006 (16 November–3 December). The summer 2005–2006 data show generally low dFe concentrations in polynya surface waters (0.10 ± 0.05 nM in upper 40 m, n = 175), consistent with previous observations. Surprisingly, our spring 2006 data reveal similar low surface dFe concentrations in the polynya (0.06 ± 0.04 nM in upper 40 m, n = 69), in association with relatively high rates of primary production (~170–260 mmol C m−2 d−1). These results indicate that the winter reserve dFe may be consumed relatively early in the growing season, such that polynya surface waters can become “iron limited” as early as November; i.e., the seasonal depletion of dFe is not necessarily gradual. Satellite observations reveal significant biomass accumulation in the polynya during summer 2006–2007, implying significant sources of “new” dFe to surface waters during this period. Possible sources of this new dFe include episodic vertical exchange, lateral advection, aerosol input, and reductive dissolution of particulate iron.
    Description: This research was supported by U.S. National Science Foundation awards OPP-0338164 to PNS, OPP- 0338350 to RBD, OPP-0440840 to MAS, OPP-0338157 to WOS, and OPP-0338097 to GRD.
    Description: 2012-06-15
    Keywords: Ross Sea ; Iron ; Phytoplankton
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 5
    Publication Date: 2022-05-26
    Description: Presented at Data Curation Network, May 15, 2020
    Description: At domain-specific data repositories, curation that strives for FAIR principles often entails transforming data submissions to improve understanding and reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification of the Frictionless Data project (https://frictionlessdata.io) in an effort to improve its data curation process efficiency. In doing so, BCO-DMO has been using the Frictionless Data Package Pipelines library (https://github.com/frictionlessdata/datapackage-pipelines) to define the processing steps that transform original submissions to final data products. Because these pipelines are defined using a declarative language they can be serialized into formal provenance data structures using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). While there may still be some curation steps that cannot be easily automated, this method is a step towards reproducible transforms that bridge the original data submission to its published state in machine-actionable ways that benefit the research community through transparency in the data curation process. BCO-DMO has built a user interface on top of these modular tools for making it easer for data managers to process submission, reuse existing workflows, and make transparent the added value of domain-specific data curation.
    Description: NSF #1924618
    Keywords: Data Curation ; Provenance ; Workflows ; Frictionless Data ; Data management ; Data repository
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 6
    Publication Date: 2022-05-26
    Description: Presented at USGS Data Management Working Group, 9, November 2020
    Description: At domain-specific data repositories, curation that strives for FAIR principles often entails transforming data submissions to improve understanding and reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification of the Frictionless Data project (https://frictionlessdata.io) in an effort to improve its data curation process efficiency. In doing so, BCO-DMO has been using the Frictionless Data Package Pipelines library (https://github.com/frictionlessdata/datapackage-pipelines) to define the processing steps that transform original submissions to final data products. Because these pipelines are defined using a declarative language they can be serialized into formal provenance data structures using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). While there may still be some curation steps that cannot be easily automated, this method is a step towards reproducible transforms that bridge the original data submission to its published state in machine-actionable ways that benefit the research community through transparency in the data curation process. BCO-DMO has built a user interface on top of these modular tools for making it easier for data managers to process submission, reuse existing workflows, and make transparent the added value of domain-specific data curation.
    Description: NSF #1924618
    Keywords: Data Curation ; Provenance ; Workflows ; Frictionless Data ; Data management ; Data repository
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 7
    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums. The definitive version was published in Frontiers in Microbiology 2 (2011): 160, doi:10.3389/fmicb.2011.00160.
    Description: The Ross Sea is home to some of the largest phytoplankton blooms in the Southern Ocean. Primary production in this system has previously been shown to be iron limited in the summer and periodically iron and vitamin B12 colimited. In this study, we examined trace metal limitation of biological activity in the Ross Sea in the austral spring and considered possible implications for vitamin B12 nutrition. Bottle incubation experiments demonstrated that iron limited phytoplankton growth in the austral spring while B12, cobalt, and zinc did not. This is the first demonstration of iron limitation in a Phaeocystis antarctica-dominated, early season Ross Sea phytoplankton community. The lack of B12 limitation in this location is consistent with previous Ross Sea studies in the austral summer, wherein vitamin additions did not stimulate P. antarctica growth and B12 was limiting only when bacterial abundance was low. Bottle incubation experiments and a bacterial regrowth experiment also revealed that iron addition directly enhanced bacterial growth. B12 uptake measurements in natural water samples and in an iron fertilized bottle incubation demonstrated that bacteria serve not only as a source for vitamin B12, but also as a significant sink, and that iron additions enhanced B12 uptake rates in phytoplankton but not bacteria. Additionally, vitamin uptake rates did not become saturated upon the addition of up to 95 pM B12. A rapid B12 uptake rate was observed after 13 min, which then decreased to a slower constant uptake rate over the next 52 h. Results from this study highlight the importance of iron availability in limiting early season Ross Sea phytoplankton growth and suggest that rates of vitamin B12 production and consumption may be impacted by iron availability.
    Description: This research was supported by NSF grants OCE-0752291, OPP-0440840, OPP-0338097, OPP-0338164, ANT-0732665, OCE-0452883, and OCE-1031271, the Center for Microbial Oceanography Research and Education (CMORE) and a National Science Foundation (NSF) Graduate Research Fellowship (2007037200) and an Environmental Protection Agency STAR Fellowship to EMB (F6E20324).
    Keywords: Iron limitation ; Vitamin B12 ; Ross Sea ; Colimitation ; Bacteria ; Phytoplankton ; Iron fertilization
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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