BCO-DMO Quick Guide

BCO-DMO, a repository funded by the National Science Foundation (NSF), supports the oceanographic research community’s data needs throughout the entire data life cycle. This guide describes the services available from BCO-DMO from proposal to preservation and highlights phases where researchers engage significantly with the office.Curating and providing open access to research data is a collaborative process. This process may be thought of as a life cycle with data passing through various phases. Each phase has its own associated actors, roles, and critical activities. Good data management practices are necessary for all phases, from proposal to preservation.NSF #143557

Towards capturing data curation provenance using Frictionless Data Package Pipelines [poster]

Presented at FORCE2018 Conference, Montreal, Canada, October 10-12, 2018. FORCE: Future of Research Communications and e-ScholarshipAt 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.NSF #143557

Towards Capturing Provenance of the Data Curation Process at Domain-specific Repositories

Presented at AGU Fall Meeting, American Geophysical Union, Washington, D.C., 10 – 14 Dec 2018Data 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.NSF #143557

Biological & Chemical Oceanography Data Management Office : a domain-specific repository for oceanographic data from around the world [poster]

Presented at AGU Ocean Sciences, 11 - 16 February 2018, Portland, ORThe Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a domain-specific digital data repository that works with investigators funded under the National Science Foundation’s Division of Ocean Sciences and Office of Polar Programs to manage their data free of charge. Data managers work closely with investigators to satisfy their data sharing requirements and to develop comprehensive Data Management Plans, as well as to ensure that their data will be well described with extensive metadata creation. Additionally, BCO-DMO offers tools to find and reuse these high-quality data and metadata packages, and services such as DOI generation for publication and attribution. These resources are free for all to discover, access, and utilize. As a repository embedded in our research community, BCO-DMO is well positioned to offer knowledge and expertise from both domain trained data managers and the scientific community at large. BCO-DMO is currently home to more than 9000 datasets and 900 projects, all of which are or will be submitted for archive at the National Centers for Environmental Information (NCEI). Our data holdings continue to grow, and encompass a wide range of oceanographic research areas, including biological, chemical, physical, and ecological. These data represent cruises and experiments from around the world, and are managed using community best practices, standards, and technologies to ensure accuracy and promote re-use. BCO-DMO is a repository and tool for investigators, offering both ocean science data and resources for data dissemination and publication.NSF #143557

Capturing Provenance of Data Curation at BCO-DMO

Presented at USGS Data Management Working Group, 9, November 2020At 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.NSF #192461

Capturing Provenance of Data Curation at BCO-DMO

Presented at Data Curation Network, May 15, 2020At 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.NSF #192461

Ovariectomy results in differential shifts in gut microbiota in low versus high aerobic capacity rats

The increased risk for cardiometabolic disease with the onset of menopause is widely studied and likely precipitated by the decline in endogenous estradiol (E2), yet the precise mechanisms are unknown. The gut microbiome is involved in estrogen metabolism and has been linked to metabolic disease, suggesting its potential involvement in the postmenopausal phenotype. Furthermore, menopause‐associated risk factors, as well as gut ecology, are altered with exercise. Therefore, we studied microbial changes in an ovariectomized (OVX vs. Sham) rat model of high (HCR) and low (LCR) intrinsic aerobic capacity (n = 8–10/group) in relation to changes in body weight/composition, glucose tolerance, and liver triglycerides (TG). Nine weeks after OVX, HCR rats were moderately protected against regional adipose tissue gain and liver TG accumulation (P < 0.05 for both). Microbial diversity and number of the Bacteroidetes phylum were significantly increased in LCR with OVX, but unchanged in HCR OVX relative to Sham. Plasma short‐chain fatty acids (SCFA), produced by bacteria in the gut and recognized as metabolic signaling molecules, were significantly greater in HCR Sham relative to LCR Sham rats (P = 0.05) and were decreased with OVX in both groups. These results suggest that increased aerobic capacity may be protective against menopause‐associated cardiometabolic risk and that gut ecology, and production of signaling molecules such as SCFA, may contribute to the mediation.We have demonstrated modest protection from the metabolic effects of surgical menopause (ovariectomy, OVX) in rats with increased aerobic capacity (high running capacity, HCR) relative to those with low aerobic capacity (low running capacity, LCR). These results are associated with significant differences in gut microbiota and their products (short chain fatty acids) between the two groups.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/113123/1/phy212488.pd

The light and the dark : Polarity in 'Christabel' and Pierre

That polar opposites are a condition of human experience is indicated in both Eastern and Western philosophy. My intention is not to explore the myriad facets of polarity, but to focus on this principle that was such a powerful force of motivation in the worlds of Coleridge and Melville as they experienced the conflict of light and darkness that surges from the unconscious activity of the mind, ever striving toward reconciliation. This study encompasses Samuel Taylor Coleridge's "Christabel" and Herman Melville's Pierre, only a segment of their search to synthesize the inescapable conflicts of existence, but one that significantly reflects the attempt both men made to transcend this opposition: The primitive darkness as seen in Geraldine and Isabel joins the incompleteness of light and innocence represented by Christabel and Lucy and forms a wider vision of reality. The bond between the two men lies deeper than the influence one man had on the other, for their symbolic worlds spiral downward to that creative and archaic, psychic center that reaches back to the beginning of man. However, it was the ability of Coleridge to articulate this struggle between the primal unconscious and the guiding intellect, in symbols that touched a responding cord in Melville's mind and brought forth Pierre, that is so ancestrally akin to "Christabel."English, Department o

Using the Theory of Planned Behavior to Elicit Restaurant Employee Beliefs about Food Safety: Using Surveys Versus Focus Groups

Within the framework of the theory of planned behavior (Ajzen, 1991), this study compared the relative usefulness of utilizing a focus group or survey methodology when eliciting restaurant employees’ beliefs about performing three important food safety behaviors (handwashing, using thermometers, and cleaning and sanitizing work surfaces). Restaurant employees completed both a survey and focus group interview assessing their beliefs about food safety. Results obtained through surveys were observed to be comparable to focus groups, suggesting researchers employ the less expensive and less time-consuming survey methodology. The strengths and weaknesses of each method are discussed. Specific salient beliefs (e.g., advantages, barriers, etc.) about the behaviors offer implications for workplace food safety interventions and training

Effects of observing employees for food safety compliance rates.

Research investigating foodservice employees’ compliance with food safety guidelines often utilizes observational methodology where an observer is present and recording employees’ behaviors as they work. Research must determine if the observer’s presence influences employees who are trained in food safety and those who are not. A group who had received a four‐hour ServSafe® food safety training course and a control group were included in the study (N=252). Both groups’ compliance rates were higher during the first hour of the observation compared to the last two hours of the observation. Implications for foodservice managers, researchers, and health inspectors are discussed