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ImmPort, toward repurposing of open access immunological assay data for translational and clinical research

Sanchita Bhattacharya, Patrick Dunn, Cristel G. Thomas, Barry Smith, Henry Schaefer, Jieming Chen, Zicheng Hu, Kelly A. Zalocusky, Ravi D. Shankar, Shai S. Shen-Orr, Elizabeth Thomson, Jeffrey Wiser (+1 others)
2018 Scientific Data  
The ImmPort ecosystem consists of four components-Private Data, Shared Data, Data Analysis, and Resources-for data archiving, dissemination, analyses, and reuse.  ...  To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings.  ...  Acknowledgements This work was supported by the National Institute of Allergy and Infectious Diseases (Bioinformatics Support Contract HHSN272201200028C) and by the National Institute for General Medical  ... 
doi:10.1038/sdata.2018.15 pmid:29485622 pmcid:PMC5827693 fatcat:o4xynhhv3vgqnfdghmqrh4rmie

Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium

Vladimir Brusic, Raphael Gottardo, Steven H Kleinstein, Mark M Davis
2014 Nature Biotechnology  
Each HIPC research center also has biostatistics and bioinformatics experts who analyze and organize these data.  ...  A central HIPC goal is sharing data as widely and freely as possible to promote exploratory, descriptive and predictive research.  ... 
doi:10.1038/nbt.2777 pmid:24441472 pmcid:PMC4294529 fatcat:uapqk35y2jdyffgietm3uj2peu

Opportunities and Challenges in Democratizing Immunology Datasets

Sanchita Bhattacharya, Zicheng Hu, Atul J. Butte
2021 Frontiers in Immunology  
In the last couple of decades, advancements in data acquisition techniques have presented opportunities to explore untapped areas of immunological research.  ...  We present use cases for repurposing open-access immunology datasets with advanced machine learning applications and more.  ...  Patrick Dunn and Anupama Gururaj, Katherine Hypes, and Elizabeth Thomson for their valuable comments. The graphics for "Measurement Techniques" in Figure 1 were created with BioRender.com.  ... 
doi:10.3389/fimmu.2021.647536 pmid:33936065 pmcid:PMC8086961 fatcat:x5yp4fhgzfdabjmlqjr6spzuly

Enabling precision medicine in neonatology, an integrated repository for preterm birth research

Marina Sirota, Cristel G. Thomas, Rebecca Liu, Maya Zuhl, Payal Banerjee, Ronald J. Wong, Cecele C. Quaintance, Rite Leite, Jessica Chubiz, Rebecca Anderson, Joanne Chappell, Mara Kim (+14 others)
2018 Scientific Data  
Acknowledgements Research reported in this publication was supported by the National Institute of Allergy and Infectious Diseases (Bioinformatics Support Contract HHSN272201200028C) and the March of Dimes  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or the March of Dimes.  ...  Since 2004, NG has been the prime contractor for the ImmPort 24 database and data-sharing portal, working with researchers at UCSF and Stanford to ensure that NIAID-funded discoveries serve as the foundation  ... 
doi:10.1038/sdata.2018.219 pmid:30398470 pmcid:PMC6219406 fatcat:2zwzpk2azfayzm54muucbqkc74

An Ontology-Based Framework for Clinical Research Databases

Richard H. Scheuermann, Megan Kong, Carl Dahlke, David Karp
2009 Nature Precedings  
-basic, translational and clinical researchImmunology Database and Analysis Portal (ImmPort) -www.ImmPort.org -Archive and manage basic and clinical research data -Analyze experiment data -Integrate  ...  exams -Blood draw, PBMC isolation -Treatment, surgery (interventions) • Semi-public web-based database and analysis portal -Multi-level access control -Data sharingData -Reference data  ... 
doi:10.1038/npre.2009.3482.1 fatcat:robckvsulzehxhbwbuh7hyvxs4

An Ontology-Based Framework for Clinical Research Databases

Richard H. Scheuermann, Richard H. Scheuermann, Megan Kong, Carl Dahlke, David Karp
2009 Nature Precedings  
-basic, translational and clinical researchImmunology Database and Analysis Portal (ImmPort) -www.ImmPort.org -Archive and manage basic and clinical research data -Analyze experiment data -Integrate  ...  exams -Blood draw, PBMC isolation -Treatment, surgery (interventions) • Semi-public web-based database and analysis portal -Multi-level access control -Data sharingData -Reference data  ... 
doi:10.1038/npre.2009.3482 fatcat:j3xpnzyzqzagpa7jud66ihyy7a

Ethical and Practical Issues Associated with Aggregating Databases

David R Karp, Shelley Carlin, Robert Cook-Deegan, Daniel E Ford, Gail Geller, David N Glass, Hank Greely, Joel Guthridge, Jeffrey Kahn, Richard Kaslow, Cheryl Kraft, Kathleen MacQueen (+3 others)
2008 PLoS Medicine  
The authors are listed in alphabetical order, except for DRK and JS. Each author attended the meeting, took part in the discussions, and contributed to the text.  ...  Acknowledgments This article summarizes a workshop organized by the University of Texas Southwestern Medical Center at Dallas as part of the Bioinformatics Integration Support Contract.  ...  It also requires that data be shared among the collaborators. Modern bioinformatics platforms have the capacity to combine datasets and store them for re-analysis.  ... 
doi:10.1371/journal.pmed.0050190 pmid:18816162 pmcid:PMC2553818 fatcat:tgh3j6jomvbv3dcegnhuyly6ey

The 10,000 Immunomes Project: A Resource for Human Immunology

Matthew J. Kan, Kelly Zalocusky, Zicheng Hu, Patrick Dunn, Elizabeth Thomson, Jeffrey Wiser, Sanchita Bhattacharya, Atul Butte
2018 Journal of Allergy and Clinical Immunology  
Subject-level data is available for interactive visualization and download at http://10kImmunomes.org/.  ...  study data and protocols.  ...  ImmPort: Shared research data for bioinformatics and immunology. In: 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2015. p. 607-10. 22. Mackay CR.  ... 
doi:10.1016/j.jaci.2017.12.857 fatcat:4rxdcykkibc4xjqwgvuedxnpaq

Toward an ontology-based framework for clinical research databases

Y. Megan Kong, Carl Dahlke, Qun Xiang, Yu Qian, David Karp, Richard H. Scheuermann
2011 Journal of Biomedical Informatics  
In order to capture and manage this diverse array of data, we have developed the Ontology-Based eXtensible data model (OBX) to serve as a framework for clinical research data in the Immunology Database  ...  and Analysis Portal (ImmPort).  ...  Supported by NIH N01AI40076 and U54RR023468.  ... 
doi:10.1016/j.jbi.2010.05.001 pmid:20460173 pmcid:PMC2953614 fatcat:sadmjdx7nffxbmk7wz555lw4xe

The 10,000 Immunomes Project: A resource for human immunology [article]

Kelly A. Zalocusky, Matthew J. Kan, Zicheng Hu, Patrick Dunn, Elizabeth Thomson, Jeffrey Wiser, Sanchita Bhattacharya, Atul J. Butte
2017 bioRxiv   pre-print
Subject-level data is available for interactive visualization and download at http://10kImmunomes.org/.  ...  study data and protocols.  ...  ImmPort: Shared research data for bioinformatics and immunology. In: 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2015. p. 607-10. 22. Mackay CR.  ... 
doi:10.1101/180489 fatcat:kxlayjybmnbf7kcjyaf2omoyhu

Reanalysis of the Rituximab in ANCA-Associated Vasculitis trial identifies granulocyte subsets as a novel early marker of successful treatment

Mazen Nasrallah, Yannick Pouliot, Bjoern Hartmann, Patrick Dunn, Elizabeth Thomson, Jeffrey Wiser, Atul J. Butte
2015 Arthritis Research & Therapy  
Methods: Clinical and flow cytometry data from the RAVE trial were downloaded from the Immunology Database and Analysis Portal and Immune Tolerance Network TrialShare public repositories.  ...  Flow cytometry data were analyzed using validated automated gating and joined with clinical data.  ...  The authors thank Ashley Xia and Quan Chen at the National Institute of Allergy and Infectious Diseases for their oversight of the bioinformatics support contract.  ... 
doi:10.1186/s13075-015-0778-z pmid:26387933 pmcid:PMC4576403 fatcat:eztbifjxh5cxhl5zas47hkfgfu

Application of Machine Learning for Cytometry Data

Zicheng Hu, Sanchita Bhattacharya, Atul J. Butte
2022 Frontiers in Immunology  
Here, we review the existing machine learning applications for analyzing cytometry data and highlight the importance of publicly available cytometry data that enable researchers to develop and validate  ...  Modern cytometry technologies present opportunities to profile the immune system at a single-cell resolution with more than 50 protein markers, and have been widely used in both research and clinical settings  ...  ImmPort is a data repository for sharing clinical and basic research data from immunology-related studies (47). As of Sep 2021, 495 studies are shared on Immport.  ... 
doi:10.3389/fimmu.2021.787574 pmid:35046945 pmcid:PMC8761933 fatcat:e5mjjybfprfkbgrcincmbbimp4

The 10,000 Immunomes Project: Building a Resource for Human Immunology

Kelly A. Zalocusky, Matthew J. Kan, Zicheng Hu, Patrick Dunn, Elizabeth Thomson, Jeffrey Wiser, Sanchita Bhattacharya, Atul J. Butte
2018 Cell Reports  
Here, we present the 10,000 Immunomes Project (10KIP), a framework for growing a diverse human immunology reference, from ImmPort, a publicly available resource of subject-level immunology data.  ...  All data in the resource are available for visualization and download at http://10kimmunomes.org/.  ...  We would also like to acknowledge all of the original data contributors who, by submitting their individual-level data to ImmPort, made this work possible.  ... 
doi:10.1016/j.celrep.2018.09.021 pmid:30304689 pmcid:PMC6263160 fatcat:usoskm537bachnyzxvqdpyuyfe

Computational and Systems Immunology: A Student's Perspective

Zinaida Good, Jacob Glanville, Marvin H. Gee, Mark M. Davis, Purvesh Khatri
2019 Trends in immunology  
The big data revolution has transformed the landscape of immunology research.  ...  As inaugural students of Stanford's new Computational and Systems Immunology PhD track, we share our experiences and advice with other institutions considering a similar program.  ...  computer science, statistics, and bioinformatics.  ... 
doi:10.1016/j.it.2019.06.006 pmid:31288986 pmcid:PMC7035103 fatcat:6qjfjmuj5fh2figseslsv5dkgi

A Pilot Study Showing a Stronger H1N1 Influenza Vaccination Response during Pregnancy in Women Who Subsequently Deliver Preterm

Sandra Andorf, Sanchita Bhattacharya, Brice Gaudilliere, Gary M. Shaw, David K. Stevenson, Atul J. Butte, Marina Sirota
2019 Journal of Reproductive Immunology  
Although a variety of social, environmental, and maternal factors have been implicated in PTB, causes of preterm labor have remained largely unknown.  ...  There is evidence of effectiveness and safety of influenza vaccination during pregnancy, however fewer studies have looked at vaccination response as an indicator of an innate host response that may be  ...  We would like to thank the ImmPort team especially Patrick Dunn, Elizabeth Thomson and Henry Schaefer as well as the authors of the original data for helping us clarify data elements.  ... 
doi:10.1016/j.jri.2019.02.004 pmid:30852461 pmcid:PMC6456418 fatcat:b6lw5b7hm5e7vmk4ebif33owlm
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