scholarly journals Optimizing Open Data to Support One Health: Best Practices to Ensure Interoperability of Genomic Data from Microbial Pathogens

2020 ◽  
Author(s):  
Ruth E. Timme ◽  
William J. Wolfgang ◽  
Maria Balkey ◽  
Sai Laxmi Gubbala Venkata ◽  
Robyn Randolph ◽  
...  
Keyword(s):  
Best Practices ◽  
One Health ◽  
Open Data ◽  
Holistic Approach ◽  
Interdisciplinary Cooperation ◽  
Microbial Pathogens ◽  
Health Goals ◽  
Public Data ◽  
Open Access Database ◽  
Pathogen Surveillance

The holistic approach of One Health, which sees human, animal, plant, and environmental health as a unit, rather than discrete parts, requires not only interdisciplinary cooperation, but standardized methods for communicating and archiving data, enabling participants to easily share what they have learned and allow others to build upon their findings.Ongoing work by NCBI and the GenomeTrakr project illustrates how open data platforms can help meet the needs of federal and state regulators, public health laboratories, departments of agriculture, and universities. Here we describe how microbial pathogen surveillance can be transformed by having an open access database along with Best Practices for contributors to follow. First, we describe the open pathogen surveillance framework, hosted on the NCBI platform. We cover the current community standards for WGS quality, provide an SOP for assessing your own sequence quality and recommend QC thresholds for all submitters to follow. We then provide an overview of NCBI data submission along with step by step details. And finally, we provide curation guidance and an SOP for keeping your public data current within the database. These Best Practices can be models for other open data projects, thereby advancing the One Health goals of Findable, Accessible, Interoperable and Re-usable (FAIR) data.

scholarly journals Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Ruth E. Timme ◽  
William J. Wolfgang ◽  
Maria Balkey ◽  
Sai Laxmi Gubbala Venkata ◽  
Robyn Randolph ◽  
...  
Keyword(s):  
Best Practices ◽  
One Health ◽  
Open Data ◽  
Holistic Approach ◽  
Interdisciplinary Cooperation ◽  
Health Goals ◽  
Public Data ◽  
Open Access Database ◽  
The One ◽  
Pathogen Surveillance

Abstract The holistic approach of One Health, which sees human, animal, plant, and environmental health as a unit, rather than discrete parts, requires not only interdisciplinary cooperation, but standardized methods for communicating and archiving data, enabling participants to easily share what they have learned and allow others to build upon their findings. Ongoing work by NCBI and the GenomeTrakr project illustrates how open data platforms can help meet the needs of federal and state regulators, public health laboratories, departments of agriculture, and universities. Here we describe how microbial pathogen surveillance can be transformed by having an open access database along with Best Practices for contributors to follow. First, we describe the open pathogen surveillance framework, hosted on the NCBI platform. We cover the current community standards for WGS quality, provide an SOP for assessing your own sequence quality and recommend QC thresholds for all submitters to follow. We then provide an overview of NCBI data submission along with step by step details. And finally, we provide curation guidance and an SOP for keeping your public data current within the database. These Best Practices can be models for other open data projects, thereby advancing the One Health goals of Findable, Accessible, Interoperable and Re-usable (FAIR) data.

scholarly journals Adequacy of prenatal care, diagnosis and treatment of syphilis in pregnancy: a study with open data from Brazilian state capitals

2020 ◽  
Vol 36 (1) ◽  
Author(s):  
Adele Schwartz Benzaken ◽  
Gerson Fernando Mendes Pereira ◽  
Alessandro Ricardo Caruso da Cunha ◽  
Flavia Moreno Alves de Souza ◽  
Valéria Saraceni
Keyword(s):  
Prenatal Care ◽  
Skin Color ◽  
Congenital Syphilis ◽  
Open Data ◽  
Family Health ◽  
Diagnosis And Treatment ◽  
Benzathine Penicillin ◽  
White Skin ◽  
Public Data ◽  
Adequacy Of Prenatal Care

Abstract: To assess the adequacy of prenatal care offered in the Brazilian capital cities and the diagnosis of gestational syphilis through public data from health information systems. The modified Kotelchuck index for adequacy of prenatal care was built using Brazilian Information System on Live Births (SINASC) data. Data on gestational syphilis, congenital syphilis, estimated population coverage by the Family Health Strategy (FHS), the Municipal Human Development Index (MHDI) and data from National Program for Access and Quality Improvement in Primary Care (PMAQ-AB) were accessed in public sites. The profile of pregnant women associated with inadequate care was assessed by logistic regression. In total, 685,286 births were analyzed. Only 2.3% of women did not attend prenatal appointments. The mean adequacy was 79.7%. No correlation was found between adequacy of prenatal care and FHS coverage (p = 0.172), but a positive correlation was found with the MHDI (p < 0.001). Inadequacy of prenatal care was associated with age below 20 years old, schooling less than 4 years, non-white skin color and not having a partner. Among the congenital syphilis cases, 17.2% of mothers did not attend prenatal care. Gestational syphilis more often affected vulnerable women, including a higher proportion of adolescents, women with low schooling, and women of non-white color. The PMAQ-AB showed a median availability of 27.3% for syphilis rapid tests, 67.7% for benzathine penicillin, and 86.7% for benzathine penicillin administration by health teams. The use of public data showed a low adequacy of prenatal care in Brazilian capitals, denoting insufficient quality for the diagnosis and treatment of gestational syphilis, despite the availability of supplies. Continuous monitoring can be carried out using public data, indicating to local strategies to eliminate congenital syphilis.

PHAROS: A digital research space for photo archives

2020 ◽  
Vol 45 (1) ◽  
pp. 2-11
Author(s):  
Costanza Caraffa ◽  
Emily Pugh ◽  
Tracy Stuber ◽  
Louisa Wood Ruby
Keyword(s):  
Image Analysis ◽  
Best Practices ◽  
Digital Image ◽  
Open Data ◽  
Linked Open Data ◽  
Historical Research ◽  
Research Directions ◽  
Prospective Research ◽  
Computational Image Analysis ◽  
Modern Technologies

The PHAROS consortium of fourteen international art historical photo archives is digitizing the over 20 million images (with accompanying documentation) in its combined collections and has begun to construct a common access platform using Linked Open Data and the ResearchSpace software. In addition to resulting in a rich and substantial database of images for art-historical research, the PHAROS initiative supports the development of shared standards for mapping and sharing photo archive metadata, as well as for best practices for working with large digital image collections and conducting computational image analysis. Moreover, alongside their digitization efforts, PHAROS member institutions are considering the kinds of art-historical questions the resulting database of images could be used to research. This article indicates some of the prospective research directions stimulated by modern technologies, with the aim of exploring the epistemological potential of photographic archives and challenging the boundaries between the analogue and the digital.

Pertinence and Feasibility of a Unifying Holistic Approach of IT Governance

2015 ◽  
Vol 6 (1) ◽  
pp. 1-15
Author(s):  
Mohamed Makhlouf ◽  
Oihab Allal-Cherif
Keyword(s):  
Information System ◽  
Action Research ◽  
Best Practices ◽  
Design Science ◽  
It Governance ◽  
Holistic Approach ◽  
Literature Study ◽  
Telecommunication Operators

In accordance with the Design Science percepts, the authors present in this paper an approach that aims to give a holistic unifying framework that ensures consistency and coherence between the existing IT governance approaches and mechanisms. It considers the advances and best practices suggested by COBIT ITIL, etc. Therefore, it proposes an operational implementation and instantiation of information system of IT governance based on SOA architecture. It meets the requirements posed by gaps in the research on IT governance, which have been proven by the literature study. as well as the managerial problems highlighted by a two-year in-depth case study conducted inside one of the largest telecommunication operators in Europe. The relevance and feasibility of this approach have been proven by the implementation of this approach in a another two-year in-depth action research case study inside another large European telecommunications operator.

scholarly journals Open Data Policies among Library and Information Science Journals

Publications ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 25
Author(s):  
Brian Jackson
Keyword(s):  
Information Science ◽  
Open Data ◽  
Research Data ◽  
Data Availability ◽  
Academic Publishing ◽  
Library And Information Science ◽  
Data Archiving ◽  
Open Research ◽  
Open Access Journals ◽  
Public Data

Journal publishers play an important role in the open research data ecosystem. Through open data policies that include public data archiving mandates and data availability statements, journal publishers help promote transparency in research and wider access to a growing scholarly record. The library and information science (LIS) discipline has a unique relationship with both open data initiatives and academic publishing and may be well-positioned to adopt rigorous open data policies. This study examines the information provided on public-facing websites of LIS journals in order to describe the extent, and nature, of open data guidance provided to prospective authors. Open access journals in the discipline have disproportionately adopted detailed, strict open data policies. Commercial publishers, which account for the largest share of publishing in the discipline, have largely adopted weaker policies. Rigorous policies, adopted by a minority of journals, describe the rationale, application, and expectations for open research data, while most journals that provide guidance on the matter use hesitant and vague language. Recommendations are provided for strengthening journal open data policies.

Data dissemination best practices and challenges identified through NOAA’s Big Data Project

2020 ◽  
Author(s):  
Meredith Richardson ◽  
Ed Kearns ◽  
Jonathan O'Neil
Keyword(s):  
Big Data ◽  
Best Practices ◽  
Data Dissemination ◽  
Public And Private ◽  
Data Formats ◽  
Data Authentication ◽  
Start Up ◽  
Public Data ◽  
Amazon Web Services ◽  
Public And Private Stakeholders

&lt;p&gt;Through satellites, ships, radars, and weather models, the National Oceanic and Atmospheric Administration (NOAA) generates and handles tens of terabytes of data per day. Many of NOAA&amp;#8217;s key datasets have been made available to the public through partnerships with Google, Microsoft, Amazon Web Services, and more as part of the Big Data Project (BDP). This movement of data to the Cloud has enabled access for researchers from all over the world to vast amounts of NOAA data, initiating a new form of federal data management as well as exposing key challenges for the future of open-access data. NOAA researchers have run into challenges of providing &amp;#8220;analysis-ready&amp;#8221; datasets to which researchers from varying fields can easily access, manipulate, and use for different purposes. This issue arises as there is no agreed-upon format or method of transforming traditional datasets for the cloud across research communities, with each scientific field or start up expressing differing data formatting needs (cloud-optimized, cloud-native, etc.). Some possible solutions involve changing data formats into those widely-used throughout the visualization community, such as Cloud-Optimized GeoTIFF. Initial findings have led NOAA to facilitate roundtable discussions with researchers, public and private stakeholders, and other key members of the data community, to encourage the development of best practices for the use of public data on commercial cloud platforms. Overall, by uploading NOAA data to the Cloud, the BDP has led to the recognition and ongoing development of new best practices for data authentication and dissemination and the identification of key areas for targeting collaboration and data use across scientific communities.&lt;/p&gt;

scholarly journals The story of the sixth myth of open data and open government

2015 ◽  
Vol 9 (1) ◽  
pp. 35-51 ◽  
Author(s):  
Ann-Sofie Hellberg ◽  
Karin Hedström
Keyword(s):  
Local Level ◽  
Empirical Studies ◽  
Open Data ◽  
Data Reuse ◽  
Open Government ◽  
Content Type ◽  
The Public ◽  
Public Data ◽  
Competition Process ◽  
Public Organisations

Purpose – The aim of this paper is to describe a local government effort to realise an open government agenda. This is done using a storytelling approach. Design/methodology/approach – The empirical data are based on a case study. The authors participated in, as well as followed, the process of realising an open government agenda on a local level, where citizens were invited to use open public data as the basis for developing apps and external Web solutions. Based on an interpretative tradition, they chose storytelling as a way to scrutinise the competition process. In this paper, they present a story about the competition process using the story elements put forward by Kendall and Kendall (2012). Findings – The research builds on existing research by proposing the myth that the “public” wants to make use of open data. The authors provide empirical insights into the challenge of gaining benefits from open public data. In particular, they illustrate the difficulties in getting citizens interested in using open public data. Their case shows that people seem to like the idea of open public data, but do not necessarily participate actively in the data reuse process. Research limitations/implications – The results are based on one empirical study. Further research is, therefore, needed. The authors would especially welcome more studies that focus on citizens’ interest and willingness to reuse open public data. Practical implications – This study illustrates the difficulties of promoting the reuse of open public data. Public organisations that want to pursue an open government agenda can use these findings as empirical insights. Originality/value – This paper answers the call for more empirical studies on public open data. Furthermore, it problematises the “myth” of public interest in the reuse of open public data.

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