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Characterizing the Scope of Exposome Research Through Topic Modeling and Ontology Analysis

Guillermo Lopez-Campos, Philip Kiossoglou, Ann Borda, Christopher Hawthorne, Kathleen Gray, Karin Verspoor
2019 Studies in Health Technology and Informatics  
In this work, we characterize the exposome research landscape and update our previous study of formal knowledge representation approaches to this field.  ...  We applied a deductive analysis using the National Center for Biomedical Ontology Recommender for comparability of the results generated from a literature dataset and newly available ontologies with our  ...  Hawthorne is funded by a Northern Ireland Department for the Economy (DfE) postgraduate studentship Award.  ... 
doi:10.3233/shti190519 pmid:31438216 fatcat:5rryojxs4rbdvoga2g5ov767om

Human Exposome Assessment Platform - Data Management Plan

Heimo Muller, Roxana Merino, Stefan Negru, Martin Boeckhout, Evert-Neb Van Veen
2020 Zenodo  
This deliverable is the Data Management Plan (DMP) of the Human Exposome Assessment Platform (HEAP), which aims to create a technical research platform to assess the impact of the internal and external  ...  collection study The plan sets out a governance framework and strategy to cover the full data management lifecycle for all of the above-mentioned data cohorts and projects.  ...  The sequencing analysis of specimens together with metadata aims to identify and characterize risk factors that may impact risk for having disease or being healthy.  ... 
doi:10.5281/zenodo.4043110 fatcat:wiq4jptomjdtfhdpzxw72klaqu

The exposome – a new approach for risk assessment

Fenna Sillé
2020 ALTEX: Alternatives to Animal Experimentation  
Considering the complexity of exposures and, in addition, the reactions of the body to exposures - i.e., the exposome - reverses classical exposure science where the precise measurement of single or few  ...  Technological developments and synergies between approaches, quality assurance (ultimately as Good Exposome Practices), and the integration of mechanistic thinking will advance this approach.  ...  The mentioned work on computational toxicology was mainly executed by Thomas Luechtefeld during  ... 
doi:10.14573/altex.2001051 pmid:31960937 fatcat:gdjlg7c2czgchdn2cvr6upiube

4549 Reproducible Informatics for Reproducible Translational Research

Ram Gouripeddi, Katherine Sward, Mollie Cummins, Karen Eilbeck, Bernie LaSalle, Julio C. Facelli
2020 Journal of Clinical and Translational Science  
A scoping review of scoping reviews: advancing the approach and enhancing the consistency.  ...  The Sequence Ontology: a tool for the unification of genome annotations.  ...  A scoping review of scoping reviews: advancing the approach and enhancing the consistency.  ... 
doi:10.1017/cts.2020.221 fatcat:zy6wnxciinbrpa2xptw7cpdou4

Information Technology for Clinical, Translational and Comparative Effectiveness Research

C. Daniel, R. Choquet
2014 IMIA Yearbook of Medical Informatics  
Two other papers exemplify the growing role of formal representation of clinical data -in metadata repositories -and knowledge -in ontologies -for supporting the process of reusing data for clinical research  ...  Objective: To select and summarize key contributions to current research in the field of Clinical Research Informatics (CRI).  ...  Acknowledgement We would like to acknowledge the support of Martina Hutter and the reviewers in the selection process of the IMIA Yearbook.  ... 
doi:10.15265/iy-2014-0040 pmid:25123747 pmcid:PMC4287061 fatcat:dgf5qqmvbfd5rfk6j3y2kjuvgm

Computational resources associating diseases with genotypes, phenotypes and exposures

Wenliang Zhang, Haiyue Zhang, Huan Yang, Miaoxin Li, Zhi Xie, Weizhong Li
2018 Briefings in Bioinformatics  
He is interested in understanding transcriptional and translational regulation through the integrative analysis of multi-omics data.  ...  Haiyue Zhang is a research assistant in Zhongshan School of Medicine at Sun Yat-sen University. Her research is focused on building and applying ontologies for phenotypes and diseases.  ...  Table 5 . 5 Summary of different biomedical data and analysis web platforms ZFin, MGI and RGD in total 17 resources Scope refers to the major focus of the web platform.  ... 
doi:10.1093/bib/bby071 pmid:30102366 fatcat:63ijmbhgxbf6pousquyuhl3s3a

Use of an Exposome Approach to Understand the Effects of Exposures From the Natural, Built, and Social Environments on Cardio-Vascular Disease Onset, Progression, and Outcomes

Paul D. Juarez, Darryl B. Hood, Min-Ae Song, Aramandla Ramesh
2020 Frontiers in Public Health  
The exposome represents the totality of exogenous (external) and endogenous (internal) exposures from conception onwards, simultaneously distinguishing, characterizing, and quantifying etiologic, mediating  ...  The exposome is a measure of all the exposures of an individual across the life course and the relationship of those exposures to health effects.  ...  Most of the studies pertaining to development of transcriptomic biomarkers have been carried out in animal models, which we have not addressed here as it is beyond the scope of this review.  ... 
doi:10.3389/fpubh.2020.00379 pmid:32903514 pmcid:PMC7437454 fatcat:avxm7oaehbhy7jsvpcszsc6une

Integrative concepts and practices of health in transdisciplinary social ecology

Timo Assmuth, Xianwen Chen, Christopher Degeling, Tari Haahtela, Katherine N. Irvine, Hans Keune, Richard Kock, Salla Rantala, Simon Rüegg, Suvi Vikström
2019 Socio-Ecological Practice Research  
Through a semi-systematic evaluation of knowledge generation in scientific publications (comprised of literature reviews, conceptual models and analyses of communities of practice), we show how integrative  ...  , expanding their scope and linking them better.  ...  To characterize the development of concepts and their uses, we employed conceptual models, drew on the previous literature, and evaluated the development of knowledge empirically by coupled bibliometric  ... 
doi:10.1007/s42532-019-00038-y fatcat:quxpvnoqunf7zgfxiponsmorea

Charting a future for epidemiologic training

Ross C. Brownson, Jonathan M. Samet, Gilbert F. Chavez, Megan M. Davies, Sandro Galea, Robert A. Hiatt, Carlton A. Hornung, Muin J. Khoury, Denise Koo, Vickie M. Mays, Patrick Remington, Laura Yarber
2015 Annals of Epidemiology  
Purpose-To identify macro level trends that are changing the needs of epidemiologic research and practice and to develop and disseminate a set of competencies and recommendations for epidemiologic training  ...  Conclusion-Addressing these issues through curricular change is needed to allow the field of epidemiology to more fully reach and sustain its full potential to benefit population health and remain a scientific  ...  Acknowledgments The authors are grateful for the input of Ms. Anna Hardy and Pam Hipp and Drs. David Celentano, Steve Goodman, Kim Johnson, and Andy Olshan.  ... 
doi:10.1016/j.annepidem.2015.03.002 pmid:25976024 pmcid:PMC4646613 fatcat:fhk5dwdq6bhkzmamevepmmjgfi

The informational stance: Philosophy and logic. Part I. The basic theories

Wu Kun, Joseph E. Brenner
2013 Logic and Logical Philosophy  
In Part II [WuB14], we develop the relation between information and social value as a basis for the ethical development of the emerging Information Society.  ...  In the 80's, Wu Kun proposed a "The Basic Theory of the Philosophy of Information", which became available in English only in 2010.  ...  structure of its related ontology, • a two-level framework of relational analysis.  ... 
doi:10.12775/llp.2013.019 fatcat:q2ajarkz3zhotbizqj4czy466i

Biomarker discovery in mass spectrometry-based urinary proteomics

Samuel Thomas, Ling Hao, William A. Ricke, Lingjun Li
2016 PROTEOMICS - Clinical Applications  
Urinary proteomics has become one of the most attractive topics in disease biomarker discovery.  ...  Mass spectrometry (MS)-based proteomic analysis has advanced continuously and emerged as a prominent tool in the field of clinical bioanalysis.  ...  Acknowledgments The authors would like to thank National Institutes of Health funding through Grants P20 DK097826; R01 DK093690; and U54 DK104310.  ... 
doi:10.1002/prca.201500102 pmid:26703953 pmcid:PMC4888976 fatcat:adao77gznvb5bc5a7q57wkb6nq

Embracing microbes in exposure science

William W Nazaroff
2018 Journal of Exposure Science and Environmental Epidemiology  
Emerging knowledge creates a major opportunity to expand the scope of exposure science to incorporate the human microbiome as a target and modulator of exposure.  ...  A study committee of the National Academies of Sciences, Engineering, and Medicine has defined a research strategy to address health risks that pertain to the interaction of environmental chemicals with  ...  Interactions with the Human Microbiome, National Academy of Sciences, Engineering and Medicine.  ... 
doi:10.1038/s41370-018-0075-4 pmid:30254254 fatcat:qe3oypzijbc4vcnpir256yezae

European Landscape Of Tdm Applications Report

Stelios Piperidis, Kanella Pouli, Maria Gavriilidou, Dimitris Galanis, Juli Bakagianni
2016 Zenodo  
(mostly in terms of funded projects), the research output (in terms of scientific publications produced), the resources and tools available for TDM as well as the commercial activity (in terms of companies  ...  In this report, after a brief introduction to the different stakeholders and parameters involved in TDM, we focus on TDM in the European Union and try to paint the landscape of TDM research, development  ...  Each topic t (in our analysis) is represented by a small set of words; the ones that are more likely to belong to t according to the estimated LDA probabilities (word-topic distribution).  ... 
doi:10.5281/zenodo.1240758 fatcat:ie25jfzuqne3bc37dc5qotcyyi

Toward a Standardized Strategy of Clinical Metabolomics for the Advancement of Precision Medicine

Long, Nghi, Kang, Anh, Kim, Park, Kwon
2020 Metabolites  
Besides, we will elucidate the potential involvement of machine learning and demonstrate that the need for automated data mining algorithms to improve the quality of future research is undeniable.  ...  Our discussion reflects the current obstacles and potential solutions toward the progressing trend of utilizing metabolomics in clinical research to create the next-generation healthcare system.  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/metabo10020051 pmid:32013105 pmcid:PMC7074059 fatcat:xwbqomk26jg7fn6rgnwwq267oe

Precision Medicine Informatics: Principles, Prospects, and Challenges [article]

Muhammad Afzal, S.M. Riazul Islam, Maqbool Hussain, Sungyoung Lee
2019 arXiv   pre-print
Recent advances in technological innovations and genetics, and the growing availability of health data have set a new pace of the research and imposes a set of new requirements on different stakeholders  ...  Furthermore, the paper provides some guidelines for future research for seamless implementation and wide-scale deployment of PM based on identified open issues and associated challenges.  ...  The research emphasized on the need of extending the scope of the existing standards rather to invent a new.  ... 
arXiv:1911.01014v1 fatcat:vnmzgn5jknhjtf5hhhwzvx3gki
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