Technologies for a FAIRer use of Ocean Best Practices

The publication and dissemination of best practices in ocean observing is pivotal for multiple aspects of modern marine science, including cross-disciplinary interoperability, improved reproducibility of observations and analyses, and training of new practitioners. Often, best practices are not published in a scientific journal and may not even be formally documented, residing solely within the minds of individuals who pass the information along through direct instruction. Naturally, documenting best practices is essential to accelerate high-quality marine science; however, documentation in a drawer has little impact. To enhance the application and development of best practices, we must leverage contemporary document handling technologies to make best practices discoverable, accessible, and interlinked, echoing the logic of the FAIR data principles [1]

Redox regulation of hepatitis C in nonalcoholic and alcoholic liver

Hepatitis C virus (HCV) is an RNA virus of the Flaviviridae family that is estimated to have infected 170 million people worldwide. HCV can cause serious liver disease in humans, such as cirrhosis, steatosis, and hepatocellular carcinoma. HCV induces a state of oxidative/nitrosative stress in patients through multiple mechanisms, and this redox perturbation has been recognized as a key player in HCV-induced pathogenesis. Studies have shown that alcohol synergizes with HCV in the pathogenesis of liver disease, and part of these effects may be mediated by reactive species that are generated during hepatic metabolism of alcohol. Furthenriore, reactive species and alcohol may influence HCV replication and the outcome of interferon therapy. Alcohol consumption has also been associated with increased sequence heterogeneity of the HCV RNA sequences, suggesting multiple modes of interaction between alcohol and HCV. This review summarizes the current understanding of oxidative and nitrosative stress during HCV infection and possible combined effects of HCV, alcohol, and reactive species in the pathogenesis of liver disease. (c) 2007 Elsevier Inc. All rights reserved

A real-world look at SCM

Supply chain management (SCM) promises to become even more challenging in the months and years ahead. How are professionals in this field coping with the stresses of performing in a tough economy? And what do they see as the keys to success for the future? For the answers, the authors went to the front lines--the logistics and supply chain managers who do the job every dayThis article is published as Daugherty, Patricia J., Scott J. Grawe, and John A. Caltagirone. "A real-world look at SCM." Supply Chain Management Review July-Aug. 2010, 14(4);12-19. Posted with permission.</p

The Ocean Best Practices System-Supporting a Transparent and Accessible Ocean

The development and deployment of best practices are playing increasingly important roles in supporting ocean observing. By their nature, well-adopted and reviewed best practices facilitate interoperability, reproducibility and enhance the quality of data and information products. To be effective, best practices must be easy to discover, access and adopt. Unfortunately, a wealth of best practices is undigitized, buried in local repositories or scattered on the web. To reduce this fragmentation and to help meet the urgent and existential global challenges rapidly approaching (see, for example, UN Decade of Ocean Science for Sustainable Development), the IOC-UNESCO Ocean Best Practices System (OBPS) has been created. The OBPS was recently described from an ocean research perspective [1]. In this paper, we describe the system's underlying technology and its core mission to enable content discovery and management through fine-scale indexing via text-mining and ontology-based semantic search tools. This relies on the reuse of well-adopted community thesauri and ontologies linking knowledge across the marine domain, through to the Sustainable Development Goals. We have implemented a constellation of software modules around the core OBPS repository (OBPS-R) to create a new, powerful, and extensible resource to accelerate best practice co-development, discovery, and access through intuitive user interfaces. While the system is operational, there are still many areas where further development can enhance the support of ocean observing. We address these in this paper and we invite the broader community to contribute to our common mission's open source codebase as well as creating and contributing ocean best practices to the OBPS

Aligned semantics to advance data interoperability across the ocean value chain - from raw data to societal goals [poster]

Presented at OceanObs’19, Honolulu, HI, September 16-20, 2019The FAIR principles (Findability, Accessibility, Interoperability, Re-usability) have pervaded discussions on data across disciplines and sectors.While data Findability and Accessibility has greatly improved, considerable difficulties in scalable interoperation remain. Without significant progress, the rapidly growing stores of ocean data risk being siloed for many years to come. A key aspect of Interoperability is "semantic": using knowledge representation (KR) to translate human understanding into machine-readable form. Quality KR allows machines to "understand" what any information artifact is about and relate it to similar artifacts, enabling discovery and enhancing reuse. KR products are usually expressed as vocabularies, glossaries, thesauri, or ontologies (collectively, terminologies), each with its own costs and benefits. Ironically, most marine terminologies are, themselves, not truly interoperable. This is an unfortunate but inevitable outcome of localised and transient funding, and the lack of sustained global infrastructures.Nonetheless, voluntary consortia are addressing this issue with urgency to realise the promise of KR in ocean observation. Here, we present 1) the alignment of well-adopted marine terminologies, 2) a collective strategy for sustained interoperability, and 3) a use case featuring the IOC-UNESCO Ocean Best Practice System. Initialised by the Biological and Chemical Oceanography Data Management Office, we are interlinking terminologies from the Natural Environment Research Council's Vocabulary Server, the Open Biological and Biomedical Ontologies Foundry, and the Earth Science Information Partners. To serve the UNESCO Decade of Ocean Science for Sustainable Development, this effort includes ontologies which represent both the Essential Ocean Variables and the UN Sustainable Development Goals. Finally, we provide perspectives on what measures are needed to meet the interoperability challenge at scale over the next decade.NSF #1435578, #192461