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The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis

Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred Hero, Barry Smith, Yongqun He
2016 Journal of Biomedical Semantics  
Conclusions: The Ontology of Biological and Clinical Statistics (OBCS) is a community-based open source ontology in the domain of biological and clinical statistics.  ...  OBCS is a timely ontology that represents statistics-related terms and their relations in a rigorous fashion, facilitates standard data analysis and integration, and supports reproducible biological and  ...  The article-processing charge was paid by a discretionary fund from Dr. Robert Dysko, the director of the Unit for Laboratory Animal Medicine (ULAM) in the University of Michigan.  ... 
doi:10.1186/s13326-016-0100-2 pmid:27627881 pmcid:PMC5024438 fatcat:6tbrilbh4nd27o57n7rpqxt3oe

The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines

Jie Zheng, Huan Li, Qingzhi Liu, Yongqun He
2017 Quantitative Biology  
The community-based Ontology of Biological and Clinical Statistics (OBCS) represents and standardizes biological and clinical data and statistical methods.  ...  The study represents the first single use case of applying OBCS ontology to standardize, integrate, and use biomedical data and statistical methods.  ...  Acknowledgments The development of VO and OBCS and the vaccine modeling research was supported by a grant from the USA National Institute of Allergy and Infectious Diseases (NIAID) (R01AI081062).  ... 
pmid:30034908 pmcid:PMC6054478 fatcat:35ydwdx2xbdgdkb52osnx6acxu

The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines

Jie Zheng, Huan Li, Qingzhi Liu, Yongqun He
2017 Quantitative Biology  
The community-based Ontology of Biological and Clinical Statistics (OBCS) represents and standardizes biological and clinical data and statistical methods.  ...  Conclusions: The study represents the first single use case of applying OBCS ontology to standardize, integrate, and use biomedical data and statistical methods.  ...  ACKNOWLEDGEMENTS The development of VO and OBCS and the vaccine modeling research was supported by a grant from the USA National Institute of Allergy and Infectious Diseases (NIAID) (R01AI081062).  ... 
doi:10.1007/s40484-017-0122-5 fatcat:ax6kb4mdarfl5kaisvehcvkgiu

VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions

Edison Ong, Peter Sun, Kimberly Berke, Jie Zheng, Guanming Wu, Yongqun He
2019 BMC Bioinformatics  
The ontology-based analysis framework supports standardized representation, integration, and analysis of heterogeneous data of host responses to vaccines.  ...  We then evaluated whether the ontological VIO modeling and VIO-based statistical analysis would contribute to the enhanced vaccine investigation studies and a better understanding of vaccine response mechanisms  ...  The Ontology of Biological and Clinical Statistics (OBCS) is a community-based ontology of statistics in the biological and clinical domains [13] .  ... 
doi:10.1186/s12859-019-3194-6 pmid:31865910 pmcid:PMC6927110 fatcat:pirn34j6qzdprdgjh3uv6bbzui

Automating Population Health Studies Through Semantics and Statistics

Alexander New, Miao Qi, Shruthi Chari, Sabbir M. Rashid, Oshani Seneviratne, James P. McCusker, John S. Erickson, Deborah L. McGuinness, Kristin P. Bennett
2019 International Semantic Web Conference  
Based on our health analysis ontology and knowledge graphs, the semanticallytargeted analysis automated architecture allows analysts to rapidly and dynamically conduct studies for different health outcomes  ...  With the rapid development of the Semantic Web, machines are able to understand the contextual meaning of data, including in the field of automated semantics-driven statistical reasoning.  ...  Acknowledgements Created with support by IBM Research AI through the AI Horizons Network.  ... 
dblp:conf/semweb/NewQCRSMEMB19 fatcat:yz7u32eko5cr7bnszqzdkqliw4

OHMI: the ontology of host-microbiome interactions

Yongqun He, Haihe Wang, Jie Zheng, Daniel P. Beiting, Anna Maria Masci, Hong Yu, Kaiyong Liu, Jianmin Wu, Jeffrey L. Curtis, Barry Smith, Alexander V. Alekseyenko, Jihad S. Obeid
2019 Journal of Biomedical Semantics  
We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility  ...  Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases. Extensive HMI studies have generated large amounts of data.  ...  Hogan, Amanda Hicks, and other experts in the host-microbiome interaction community and the biomedical ontology community. We also appreciate the support by Dr.  ... 
doi:10.1186/s13326-019-0217-1 pmid:31888755 pmcid:PMC6937947 fatcat:snpj3uakvbfnlfi3hg44n7dbca

The role of metadata in reproducible computational research [article]

Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Stian Soiland-Reyes, Karthik Ram, Jane Greenberg
2021 arXiv   pre-print
Reproducible computational research (RCR) is the keystone of the scientific method for in silico analyses, packaging the transformation of raw data to published results.  ...  This potential and wide-support for the FAIR principles have motivated interest in metadata standards supporting RCR.  ...  Acknowledgements Acknowledgements We wish to thank Jian Qin and Farah Zaib Khan for their helpful comments and suggestions.  ... 
arXiv:2006.08589v2 fatcat:txxkodvwezc6bcdngu3by6wnni

Longitudinal Monitoring of Intra-Tumoural Heterogeneity Using Optical Barcoding of Patient-Derived Colorectal Tumour Models

Carolyn Shembrey, Jai Smith, Mélodie Grandin, Nathalia Williams, Hyun-Jung Cho, Christina Mølck, Corina Behrenbruch, Benjamin NJ. Thomson, Alexander G. Heriot, Delphine Merino, Frédéric Hollande
2022 Cancers  
We demonstrate that all subpopulations can be purified from complex clonal mixtures via flow cytometry, permitting the downstream isolation and analysis of any lineages of interest.  ...  In summary, we present OBC as a user-friendly, inexpensive, and high-throughput technique for monitoring intra-tumoural heterogeneity in in vitro cell culture models.  ...  & Microscopy (PMCC) and Biological Optical Microscopy Platform (University of Melbourne).  ... 
doi:10.3390/cancers14030581 pmid:35158849 pmcid:PMC8833441 fatcat:6iow6wt4vbfu3jrvokr3wy7qqy

Ontologies relevant to behaviour change interventions: a method for their development

Alison J. Wright, Emma Norris, Ailbhe N. Finnerty, Marta M. Marques, Marie Johnston, Michael P. Kelly, Janna Hastings, Robert West, Susan Michie
2020 Wellcome Open Research  
The most novel aspects of the method are the use of formal mechanisms for literature annotation and expert stakeholder review to develop and improve the ontology content.  ...  We report the creation and refinement of a method for developing ontologies that make up the Behaviour Change Intervention Ontology (BCIO).  ...  .: The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. J Biomed Semantics. 2016; 7(1): 53.  ... 
doi:10.12688/wellcomeopenres.15908.3 fatcat:pgoyfrh75vcala7f65uxrdveqm

Abstracts from the Human Genome Meeting 2018

2018 Human Genomics  
A14 Molecular Biological Elucidation of in vitro Spermatogenesis by Transcriptome Analysis Takeru Abe 1,3 , Hajime Nishimura 3 , Kazuaki Kojima 1 , Hiroyuki Sanjo 2 , Takuya Sato 1 , Harukazu Suzuki  ...  Acknowledgments We are grateful to all members of the Laboratory for Autoimmune Diseases for their expert technical assistance Acknowledgements The study was supported by the Russian Science Foundation  ...  In the Bayesian network analysis, the results showed a stable directed link from E-CpG cg05834639 to the SLC7A5 expressiona reproducibility rate of 66.8% by using the PC algorithm and a reproducibility  ... 
doi:10.1186/s40246-018-0138-6 fatcat:nl6xhsuchzgbxik4pjwjvbbkie

Towards the Interpretability of Machine Learning Predictions for Medical Applications Targeting Personalised Therapies: A Cancer Case Survey

Antonio Jesús Banegas-Luna, Jorge Peña-García, Adrian Iftene, Fiorella Guadagni, Patrizia Ferroni, Noemi Scarpato, Fabio Massimo Zanzotto, Andrés Bueno-Crespo, Horacio Pérez-Sánchez
2021 International Journal of Molecular Sciences  
However, the interpretability of machine learning predictions so that doctors can understand them, trust them and gain useful insights for the clinical practice is still rarely considered, which is a factor  ...  Among the most challenging targets of interest in medicine are cancer diagnosis and therapies but, to start this revolution, software tools need to be adapted to cover the new requirements.  ...  However, the results of clinical trials in their advanced stages must exhibit a significant improvement over standard therapy.  ... 
doi:10.3390/ijms22094394 pmid:33922356 fatcat:z3mxbx7fajge7pkyrp2odlauz4

When will the mist clear? On the Interpretability of Machine Learning for Medical Applications: a survey [article]

Antonio-Jesús Banegas-Luna, Jorge Peña-García, Adrian Iftene, Fiorella Guadagni, Patrizia Ferroni, Noemi Scarpato, Fabio Massimo Zanzotto, Andrés Bueno-Crespo, Horacio Pérez-Sánchez
2020 arXiv   pre-print
Besides, CNNs, supported by the rapid development of GPUs and tensor-oriented programming libraries, are gaining in importance.  ...  Among the most challenging targets of interest in medicine are cancer diagnosis and therapies but, to start this revolution, software tools need to be adapted to cover the new requirements.  ...  This work has been funded by grants from the European Project Horizon 2020 SC1-BHC-  ... 
arXiv:2010.00353v1 fatcat:nnl64nbxtna4riaq5ftzw5idby

Abstract of Conferences

2019 Medicine & Health  
Sample preparation is critical to the success of MALDI imaging analysis, but until now there is no consensus on a standardized protocol for analysis.  ...  Conclusion: All clinics and wards showed high level of satisfaction above the standard set.  ... 
doi:10.17576/mh.2019.s1401 fatcat:qtm5gcbzejerxhloaabed2xh54

ACNP 56th Annual Meeting: Poster Session I, December 4, 2017

2017 Neuropsychopharmacology  
However, the biological mechanisms by which PTSD increases risks for T2DM remain unclear.  ...  Methods: We recruited a sample of (N = 63) African-American women with T2DM and high rates of lifetime trauma exposure from the primary care and diabetes specialty clinic waiting rooms of Grady Memorial  ...  Network analysis (Genemania, Gene Ontology Biological Function) identified a strong contribution in the T cell apoptotic process (P-value = 0.001).  ... 
doi:10.1038/npp.2017.264 pmid:29192265 fatcat:psc2w4azgrbfhjtxe6oxrnsdaq

Deutsche Gesellschaft für Experimentelle und Klinische Pharmakologie und Toxikologie e.V

2013 Naunyn-Schmiedeberg's Archives of Pharmacology  
Acknowledgement: This work has been financially supported by DFG and Tubitak with a travel stipend to Aylin Üstündag. [1] Yu, P., Constien, R., Dear, N., Katan, M., Hanke, P., Bunney, T.D., Kunder, S.,  ...  Grosse, J., Wabnitz, P., Meyer, T.P.H., Yasuda, K., Schiemann, M., Schneider-Fresenius, C., Jagla, W., Russ, A., Popp, A., Josephs, M., Marquardt, A., Laufs, J., Schmittwolf, C., Wagner, H., Pfeffer, K., and  ...  Statistical analysis was performed by logistic regression adjusted for age and study.  ... 
doi:10.1007/s00210-013-0832-9 pmid:23334796 fatcat:vp56yyyimzfgdgrczauhpodxou
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